higlass 1.11.11 → 1.12.1

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Files changed (113) hide show
  1. package/README.md +19 -10
  2. package/app/scripts/{AddTrackDialog.js → AddTrackDialog.jsx} +27 -26
  3. package/app/scripts/{AddTrackPositionMenu.js → AddTrackPositionMenu.jsx} +18 -15
  4. package/app/scripts/{Autocomplete.js → Autocomplete.jsx} +1 -0
  5. package/app/scripts/{Button.js → Button.jsx} +7 -6
  6. package/app/scripts/CenterTiledPlot.jsx +7 -0
  7. package/app/scripts/{CenterTrack.js → CenterTrack.jsx} +42 -41
  8. package/app/scripts/ChromosomeGrid.js +8 -16
  9. package/app/scripts/CloseTrackMenu.jsx +27 -0
  10. package/app/scripts/CombinedTrack.js +16 -1
  11. package/app/scripts/{ConfigTrackMenu.js → ConfigTrackMenu.jsx} +12 -12
  12. package/app/scripts/{ConfigViewMenu.js → ConfigViewMenu.jsx} +35 -36
  13. package/app/scripts/{ConfigureSeriesMenu.js → ConfigureSeriesMenu.jsx} +2 -2
  14. package/app/scripts/{ContextMenuContainer.js → ContextMenuContainer.jsx} +5 -7
  15. package/app/scripts/ContextMenuItem.jsx +37 -0
  16. package/app/scripts/Cross.jsx +9 -0
  17. package/app/scripts/CustomTrackDialog.jsx +38 -0
  18. package/app/scripts/DataFetcher.js +6 -6
  19. package/app/scripts/{Dialog.js → Dialog.jsx} +40 -31
  20. package/app/scripts/{DragListeningDiv.js → DragListeningDiv.jsx} +10 -12
  21. package/app/scripts/{DraggableDiv.js → DraggableDiv.jsx} +25 -24
  22. package/app/scripts/{ExportLinkDialog.js → ExportLinkDialog.jsx} +2 -2
  23. package/app/scripts/{GalleryTracks.js → GalleryTracks.jsx} +10 -9
  24. package/app/scripts/{GenomePositionSearchBox.js → GenomePositionSearchBox.jsx} +23 -21
  25. package/app/scripts/HeatmapTiledPixiTrack.js +18 -30
  26. package/app/scripts/{HiGlassComponent.js → HiGlassComponent.jsx} +213 -86
  27. package/app/scripts/HorizontalChromosomeLabels.js +3 -6
  28. package/app/scripts/HorizontalHeatmapTrack.js +2 -6
  29. package/app/scripts/HorizontalRule.js +2 -0
  30. package/app/scripts/{HorizontalTiledPlot.js → HorizontalTiledPlot.jsx} +20 -19
  31. package/app/scripts/LeftTrackModifier.js +8 -0
  32. package/app/scripts/{Modal.js → Modal.jsx} +14 -9
  33. package/app/scripts/{NestedContextMenu.js → NestedContextMenu.jsx} +6 -7
  34. package/app/scripts/OSMTilesTrack.js +2 -6
  35. package/app/scripts/OverlayTrack.js +2 -0
  36. package/app/scripts/{PopupMenu.js → PopupMenu.jsx} +1 -1
  37. package/app/scripts/SearchField.js +5 -3
  38. package/app/scripts/{SeriesListItems.js → SeriesListItems.jsx} +6 -6
  39. package/app/scripts/{SeriesListMenu.js → SeriesListMenu.jsx} +29 -32
  40. package/app/scripts/Tiled1DPixiTrack.js +2 -5
  41. package/app/scripts/TiledPixiTrack.js +3 -1
  42. package/app/scripts/{TiledPlot.js → TiledPlot.jsx} +45 -17
  43. package/app/scripts/{TilesetFinder.js → TilesetFinder.jsx} +7 -7
  44. package/app/scripts/Track.js +17 -1
  45. package/app/scripts/{TrackControl.js → TrackControl.jsx} +44 -50
  46. package/app/scripts/{TrackRenderer.js → TrackRenderer.jsx} +44 -38
  47. package/app/scripts/VerticalRule.js +1 -0
  48. package/app/scripts/{VerticalTiledPlot.js → VerticalTiledPlot.jsx} +27 -18
  49. package/app/scripts/{ViewConfigEditor.js → ViewConfigEditor.jsx} +66 -58
  50. package/app/scripts/{ViewContextMenu.js → ViewContextMenu.jsx} +13 -13
  51. package/app/scripts/{ViewHeader.js → ViewHeader.jsx} +24 -23
  52. package/app/scripts/ViewportTracker2D.js +1 -2
  53. package/app/scripts/ViewportTrackerHorizontal.js +1 -2
  54. package/app/scripts/ViewportTrackerVertical.js +1 -2
  55. package/app/scripts/api.js +17 -10
  56. package/app/scripts/configs/available-for-plugins.js +4 -3
  57. package/app/scripts/configs/index.js +1 -47
  58. package/app/scripts/configs/positions-by-datatype.js +2 -0
  59. package/app/scripts/configs/primitives.js +47 -0
  60. package/app/scripts/configs/tracks-info.js +2 -2
  61. package/app/scripts/d3-context-menu.js +1 -0
  62. package/app/scripts/data-fetchers/get-data-fetcher.js +7 -2
  63. package/app/scripts/{hglib.js → hglib.jsx} +1 -1
  64. package/app/scripts/{icons.js → icons.jsx} +24 -13
  65. package/app/scripts/mixwith.js +2 -0
  66. package/app/scripts/services/tile-proxy.js +1 -5
  67. package/app/scripts/utils/abs-to-chr.js +1 -1
  68. package/app/scripts/utils/dec-to-hex-str.js +1 -1
  69. package/app/scripts/utils/dict-items.js +0 -1
  70. package/app/scripts/utils/dict-keys.js +0 -1
  71. package/app/scripts/utils/dict-values.js +0 -1
  72. package/app/scripts/utils/index.js +1 -0
  73. package/app/scripts/utils/range-query-2d.js +4 -1
  74. package/app/scripts/utils/selected-items-to-size.js +2 -3
  75. package/app/scripts/utils/{test-helpers.js → test-helpers.jsx} +32 -10
  76. package/app/scripts/utils/timeout.js +4 -1
  77. package/app/scripts/utils/value-to-color.js +14 -17
  78. package/app/scripts/worker.js +8 -4
  79. package/app/styles/GenomePositionSearchBox.module.scss +13 -15
  80. package/app/styles/HiGlass.scss +5 -5
  81. package/app/styles/TilesetFinder.css +94 -74
  82. package/app/styles/TrackControl.module.scss +17 -20
  83. package/app/styles/TrackOptions.css +23 -24
  84. package/app/styles/ViewHeader.module.scss +18 -18
  85. package/dist/hglib.css +1724 -1
  86. package/dist/hglib.js +80473 -154092
  87. package/dist/hglib.min.js +382 -2
  88. package/dist/index.html +251 -250
  89. package/package.json +57 -117
  90. package/CHANGELOG.md +0 -1415
  91. package/app/index.html +0 -273
  92. package/app/scripts/CenterTiledPlot.js +0 -5
  93. package/app/scripts/CloseTrackMenu.js +0 -25
  94. package/app/scripts/ContextMenuItem.js +0 -35
  95. package/app/scripts/Cross.js +0 -7
  96. package/app/scripts/factories/index.js +0 -1
  97. /package/app/scripts/{FixedTrack.js → FixedTrack.jsx} +0 -0
  98. /package/app/scripts/{HeatmapOptions.js → HeatmapOptions.jsx} +0 -0
  99. /package/app/scripts/{HiGlassTrackComponent.js → HiGlassTrackComponent.jsx} +0 -0
  100. /package/app/scripts/{HorizontalItem.js → HorizontalItem.jsx} +0 -0
  101. /package/app/scripts/{HorizontalTrack.js → HorizontalTrack.jsx} +0 -0
  102. /package/app/scripts/{ListWrapper.js → ListWrapper.jsx} +0 -0
  103. /package/app/scripts/{MoveableTrack.js → MoveableTrack.jsx} +0 -0
  104. /package/app/scripts/{PlotTypeChooser.js → PlotTypeChooser.jsx} +0 -0
  105. /package/app/scripts/{SeriesListSubmenuMixin.js → SeriesListSubmenuMixin.jsx} +0 -0
  106. /package/app/scripts/{SketchInlinePicker.js → SketchInlinePicker.jsx} +0 -0
  107. /package/app/scripts/{SortableList.js → SortableList.jsx} +0 -0
  108. /package/app/scripts/{TrackArea.js → TrackArea.jsx} +0 -0
  109. /package/app/scripts/{VerticalItem.js → VerticalItem.jsx} +0 -0
  110. /package/app/scripts/{VerticalTrack.js → VerticalTrack.jsx} +0 -0
  111. /package/app/scripts/hocs/{with-modal.js → with-modal.jsx} +0 -0
  112. /package/app/scripts/hocs/{with-pub-sub.js → with-pub-sub.jsx} +0 -0
  113. /package/app/scripts/hocs/{with-theme.js → with-theme.jsx} +0 -0
package/CHANGELOG.md DELETED
@@ -1,1415 +0,0 @@
1
- # Release notes
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-
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- ## v1.11.11
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-
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- - Bump terser-webpack-plugin version to fix build issue
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-
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- ## v1.11.10
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-
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- - Remove dependency on `cwise`
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- - Fix color issue in GeneAnnotation SVG export
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-
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- ## v1.11.8
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-
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- - Remove react-bootstrap from the GenomePositionSearchBox
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- - Make vertical chromosome labels as well as loading status labels readable in vertical tracks
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- - Added an option menu item for rectangle domain fill opacity
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- - Added a parameter in `zoomToGene` to allow specifying padding around gene
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- - Add data fetchers to `AVAILABLE_FOR_PLUGINS`
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- - Update track list in `AVAILABLE_FOR_PLUGINS`
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- - Correctly setup initial scales of vertical tracks when the width of a center track is zero.
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- - Config-wise, allow axis-specific location locks (e.g., lock the vertical axis in a view to the horizontal axis in another).
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- - Add `reload` implementation to `HiGlassComponenet` API.
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-
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- _[Detailed changes since v1.11.5](https://github.com/higlass/higlass/compare/v1.11.7...develop)_
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-
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- ## v1.11.7
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-
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- - Show visual clue when tileset info is not available ("Tileset info not found. ...").
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- - Properly initialize the style of 1D brushes (`viewport-projection-horizontal` and `viewport-projection-vertical`).
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-
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- _[Detailed changes since v1.11.5](https://github.com/higlass/higlass/compare/v1.11.6...v1.11.7)_
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-
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- ## v1.11.6
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-
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- - Allow implementing plugin viewport projection tracks using `config.projection`.
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- - Change the default value of `zoomLimits` to `[1, null]`, which means highest zoom resolution is 1bp.
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-
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- _[Detailed changes since v1.11.5](https://github.com/higlass/higlass/compare/v1.11.5...v1.11.6)_
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-
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- ## v1.11.5
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-
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- - Add a `zoomToGene` API that allows to zoom a HiGlass view to a location near a certain gene.
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- - Add a `suggestGene` API that returns a list of genes of top match for a given keyword based on `autocompleteServer`.
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- - Add a top-level option, `compactLayout`, that controls to allow adding vertical gaps between views.
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-
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- _[Detailed changes since v1.11.4](https://github.com/higlass/higlass/compare/v1.11.4...v1.11.5)_
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-
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- ## v1.11.4
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-
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- - Fix colorbar error on degenerate colorscale
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- - Update horizontal heatmap to regular heatmap rendering so that they can use the same options
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-
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- _[Detailed changes since v1.11.3](https://github.com/higlass/higlass/compare/v1.11.3...v1.11.4)_
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-
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- ## v1.11.3
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-
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- - Show a more comprehensive list of track types in the track config menu
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- - Break up HiGlassComponentTests
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- - Show only integer ticks in `HorizontalChromosomeLabels` tracks because it is misleading to have decimal values in genomic coordinates.
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- - Add a `reverseOrientation` option in `HorizontalChromosomeLabels` tracks to allow aligning tick labels and lines on the top or left.
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- - Make overlays SVG exportable
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- - Fix a bug that led to the app crash when `selectRows` is set to an empty array `[]`
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- - Break up and turn off some tests
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- - Fix gene annotation mouseover
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-
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- _[Detailed changes since v1.11.2](https://github.com/higlass/higlass/compare/v1.11.2...v1.11.3)_
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-
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- ## v1.11.2
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-
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- - Fix registration of plugin tracks
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- - Don't try to render names of filler annotations
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-
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- _[Detailed changes since v1.11.1](https://github.com/higlass/higlass/compare/v1.11.1...v1.11.2)_
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-
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- ## v1.11.1
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-
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- - Fix multivec SVG export
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- - Added `ChromosomeInfo` and `SearchField` classes to `AVAILABLE_TO_PLUGINS`.
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-
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- _[Detailed changes since v1.11.0](https://github.com/higlass/higlass/compare/v1.11.0...v1.11.1)_
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-
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- ## v1.11.0
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-
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- - Make gene annotations rotatable so that they can be added on the left
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- - Tracks can now modify their own dimensions by publishing `trackDimensionsModified`.
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- - Fixed a bug preventing usage of `data.url` and HorizontalMultivecTrack server-side aggregation simultaneously.
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- - Fixed a bug preventing an updated value of `track.options.selectRows` from triggering a HorizontalMultivecTrack track update when using server-side aggregation (`track.options.selectRowsAggregationMethod === 'server'`).
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- - Added the JS API `.on('geneSearch', callback)` option for subscribing to gene search events.
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- - Simplify plugin track registry
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- - Implemented plugin data fetchers.
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-
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- _[Detailed changes since v1.10.2](https://github.com/higlass/higlass/compare/v1.10.2...v1.11.0)_
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-
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- ## v1.10.2
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-
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- - Remove view config validation from `hgApi.getViewConfig()` and `hgApi.setViewConfig()` and instead move it into a new method called `hgApi.validateViewConfig(viewConfig, { verbose: false } = {})`
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-
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- _[Detailed changes since v1.10.1](https://github.com/higlass/higlass/compare/v1.10.1...v1.10.2)_
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-
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- ## v1.10.1
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-
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- - Remove text/plain encoding from tile proxy text fetcher
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- - Added the `selectRowsAggregationMethod` option for the `horizontal-multivec` track to enable server-side aggregation if set to `"server"` rather than the default `"client"`.
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- - In the view config, moved the `fileUrl` track property under the `data` property: `data: { url, server, filetype }`.
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-
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- _[Detailed changes since v1.10.0](https://github.com/higlass/higlass/compare/v1.10.0...v1.10.1)_
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-
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- ## v1.10.0
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-
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- - Fixed horizontal and vertical cross sections
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- - Changed the style for the mouse over dialog to have a maximum width of 50 and to break words so that it doesn't go off the screen if there's a very long mouseover text.
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- - Lower the default annotation height in the Gene Annotations track
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- - Colors for rules
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- - Ability to load genome position search box chromosome sizes from an arbitrary location
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- - Plugin tracks can provide their own config menu options
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- - Remove horizontal-_ and vertical-_ prefixes from track names
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- - Load matrices with "None" data transform without crashing
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- - Add a view for showing schema log messages when JSON codes are edited in a config view.
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-
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- _[Detailed changes since v1.9.5](https://github.com/higlass/higlass/compare/v1.9.5...v1.10.0)_
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-
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- ## v1.9.5
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-
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- - Removed styles for naked td tag
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- - Reader for text genbank data (i.e. not pulled from a url)
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-
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- _[Detailed changes since v1.9.4](https://github.com/higlass/higlass/compare/v1.9.4...v.1.9.5)_
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-
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- ## v1.9.4
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-
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- - Added the `resolveImmediately` parameter to the setViewConfig API call.
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- - Zooming can now be restricted by specifying `zoomLimits` in the viewconf.
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- - Fixed bug where the track config menu improperly positioned when clicked twice.
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- - Update the heatmap option interface to allow seeing the preview when a color picker is opened.
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- - Display an error message on tiles with errors in them
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- - Don't try to assign a color value scale if the colorEncoding is set to itemRgb. itemRgb means that the color is present directly in the annotation
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- - Add an option to separate the + / - strand annotations in the bedlike track
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- _[Detailed changes since v1.9.3](https://github.com/higlass/higlass/compare/v1.9.3...v.1.9.4)_
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-
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- ## v1.9.3
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-
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- - Consolidated track options of horizontal and vertical tracks
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- - Set background of new heatmap tracks in a combined track to `transparent` when added via the track context menu.
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- - Fixed bug where heatmap labels could not be hidden.
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- - The position of labels and colorbars for split heatmaps can now be changed.
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- - Use itemRgb field in bed files as the default coloring for bedlike tracks
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- _[Detailed changes since v1.9.2](https://github.com/higlass/higlass/compare/v1.9.2...v.1.9.3)_
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-
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- ## v1.9.2
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-
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- - Fixed divided tracks bug by adding denseDataExtrema
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- - Fixed divergent bar track
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- - Made the bar track compatible with the local tile fetcher
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- - Added fontColor, fontSize and fillOpacity options to BedLikeTrack
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- - Added cheat code for making the component editable (i.e. with headers)
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- - Fixed track names in config menu
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- - Keep locks on track type change
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- - Fix crashing higlass on non-existent value scale lock member
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- _[Detailed changes since v1.9.1](https://github.com/higlass/higlass/compare/v1.9.1...v1.9.2)_
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-
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- ## v1.9.1
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-
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- - Used stretchRects to ensure that there are no rendering artifacts when zooming in too far
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- - Added scaled as a potential value to the annotationHeight option
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- - Added the maxAnnotationHeight option to limit the size of annotations when using the scaled option for annotationHeight
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- - Added the fontSize option for bedlike tracks
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- - colorAnnotations are independent of valueScale
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- - Vertical zooming on BedLike annotations
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- - Added support for aggregation of `horizontal-multivec` rows by passing arrays of row indices to the `selectRows` option. With this addition also comes the track options `selectRowsAggregationMode` (for specifying an aggregation function, "mean", "sum", "variance", "deviation") and `selectRowsAggregationWithRelativeHeight` (boolean) to determine whether rows representing groups of indices have 1-unit heights or `group.length`-unit heights.
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- - Added the JS API `.on('wheel', callback)` option for subscribing to mouse wheel events.
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- _[Detailed changes since v1.9.0](https://github.com/higlass/higlass/compare/v1.9.0...v1.9.1)_
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- ## v1.9.0
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- - Support for gene annotation "filler" regions
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- - Clickable gene annotations
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- - Slightly updated gene annotation style with arrowheads at the ends
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- - Remove Content-Type headers when fetching genbank files
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- - Added the fields `xRange` and `yRange` the object returned by the JavaScript API `.getLocation()` method.
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- - Fixed blurry exported heatmap SVG graphics issue using the `image-rendering` CSS property.
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- - Enabled view-based scaling
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- - Left and right tracks can now be value scale locked
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- - Added the attributes `projectionXDomain` and `projectionYDomain` to the `viewport-projection-horizontal` and `viewport-projection-vertical`, respectively, and both to the `viewport-projection-center`, to support the case in which the `fromViewUid` attribute is undefined.
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- - Added the `.on('createSVG')` listener to the JS API, with the corresponding `.off('createSVG')`, for manipulating exported SVGs before they are returned.
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- - Added `zeroValueColor` as an option for the `horizontal-multivec` track, to specify the color mapping for zero data values.
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- - Track resizing events now trigger the `.on('viewConfig')` JS API callback.
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- - Allowed K and M notations when entering genomic coordinates in searchbox (e.g., "chr1:150M-155M").
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- - Specify raw tiles locally in the viewconf
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- _[Detailed changes since v1.8.4](https://github.com/higlass/higlass/compare/v1.8.4...v1.9.0)_
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- ## v1.8.4
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-
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- - Corrupted lock bug fix
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- - Export to SVG with no loaded tiles bug fix
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- - `selectRows` option for Horizontal Multivec Tracks
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- _[Detailed changes since v1.8.3](https://github.com/higlass/higlass/compare/v1.8.3...v1.8.4)_
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- ## v1.8.3
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- - Added "empty" track
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- _[Detailed changes since v1.8.2](https://github.com/higlass/higlass/compare/v1.8.2...v1.8.3)_
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- ## v1.8.2
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- - Fixed horizontal track not rendering properly in vertical position bug
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- _[Detailed changes since v1.8.1](https://github.com/higlass/higlass/compare/v1.8.1...v1.8.2)_
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- ## v1.8.1
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- - Prettified JS code
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- - Added `labelShowAssembly` as an option to allow hiding the assembly in track label (e.g. `hg19 |` text)
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- - Added `tickFormat` and `tickPosition` options to the chromosome labels track
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- - Enabled the colorbar slider by adding the options `colorbarPosition` and `colorbarBackgroundColor` for the `horizontal-multivec`
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- - Added release notes to docs.
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- - Added support for selecting and filtering rows of the `horizontal-multivec` track via the `selectRows` option.
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- _[Detailed changes since v1.8.0](https://github.com/higlass/higlass/compare/v1.8.0...v1.8.1)_
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- ## v1.8.0
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- - Added the option to flip 2D annotations across the diagonal
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- - Update heatmap docs with colorRange parameter
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- - Update BedLikeTrack to display strand-specific entries
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- - Added 'segment' style to the BedLikeTrack
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- - Updated default plot types when adding tracks
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- - When adding multiple tracks at once that have different datatype, each track is added with its default plot type. The plot type chooser is hidden.
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- - In `HorizontalLine1DPixiTrack`, make sure that `this.valueScale` is set when `getMouseOverHtml()` is called.
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- - VerticalRule, HorizontalRule, and CrossRule tracks included in SVG and PNG exports.
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- _[Detailed changes since v1.7.2](https://github.com/higlass/higlass/compare/v1.7.2...v1.8.0)_
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- ## v1.7.2
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- - Refactored the scroll options and `bounded` into a new property called `sizeMode`. There are now 4 different size modes, which determine the visible height of the HiGlass instance:
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- 1. `default`: the height is given by the sum of the tracks' heights
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- 2. `bounded`: tells the HiGlass component to bind the height to the parent container by dynamically adjusting the height of center tracks.
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- 3. `scroll`: will activate scrolling by stretching HiGlass' drawing surface to the extent of parent DOM element and hiding overflowing content in the x direction and allowing to scroll when content overflows in the y direction.
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- 4. `overflow`: same as `scroll` except that you can't scroll. This mode is only needed when you want to dynamically switch between scrolling and pan+zooming.
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- _[Detailed changes since v1.7.0](https://github.com/higlass/higlass/compare/v1.7.0...v1.7.2)_
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- ## v1.7.1
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- _Same as v1.7.0. This is just due to a glitch at npmjs.org._
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- ## v1.7.0
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- - Add support for scrollable views. Activate via the option `scrollable: true`. Once you activate scrollable views all views are automatically zoomfixed! See [http://localhost:8080/others/scrollable-container.html](others/scrollable-container.html) for an example.
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- - Add `option(key, value)` to the JS API for changing options. It supports getting all options when `value` is ommited and setting `scrollable`.
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- - Properly display "Loading" while loading tileset info
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- - Add support to ignore offscreen values for value scale locking by setting `ignoreOffScreenValues: true` for a lock group in `locksDict`.
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- _[Detailed changes since v1.6.12](https://github.com/higlass/higlass/compare/v1.6.12...v1.7.0)_
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- ## v1.6.12
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- - Rename React lifecycle methods according to their recommendations
266
- - Add support for borders (via the `stroke`, `strokeWidth`, `strokeOpacity`, and `strokePos` options) and outlines (via the `outline`, `outlineWidth`, `outlineOpacity`, and `outlinePos` options) to overlays. See [http://localhost:8080/apis/svg.html?/viewconfs/fancy-overlays.json](http://localhost:8080/apis/svg.html?/viewconfs/fancy-overlays.json) for an example.
267
- - Fixed horizontal rule bug (from Slack)
268
-
269
- _[Detailed changes since v1.6.11](https://github.com/higlass/higlass/compare/v1.6.11...v1.6.12)_
270
-
271
- ## v1.6.11
272
-
273
- - Overlay track bug fixes
274
- - Added `minWidth` and `minHeight` options to `overlays` for better guidance
275
- - Allow viewconf JSON to override minimum track height or width defaults, when a track specifies a `minHeight` or `minWidth` parameter
276
-
277
- _[Detailed changes since v1.6.10](https://github.com/higlass/higlass/compare/v1.6.10...v1.6.11)_
278
-
279
- ## v1.6.10
280
-
281
- - Add API call for show track chooser (`hgApi.showTrackChooser()`)
282
- - Limit icon size in plot type chooser
283
- - Add non-gzipped support to genbank-fetcher
284
- - Better error handling for genbank fetcher
285
-
286
- _[Detailed changes since v1.6.9](https://github.com/higlass/higlass/compare/v1.6.9...v1.6.10)_
287
-
288
- ## v1.6.9
289
-
290
- - Enable brushing on bar, point, and 1d-heatmap tracks
291
-
292
- _[Detailed changes since v1.6.8](https://github.com/higlass/higlass/compare/v1.6.8...v1.6.9)_
293
-
294
- ## v1.6.8
295
-
296
- - Add infrastructure for value scale zooming
297
- - Fixed the colors when dragging a track over a higlass display
298
- - Added support for value scale zooming
299
- - Added utils/track-utils to provide track functionality for use without inheritance
300
- - Implemented a genbank data fetcher for gene annotation tracks
301
-
302
- _[Detailed changes since v1.6.7](https://github.com/higlass/higlass/compare/v1.6.7...v1.6.8)_
303
-
304
- ## v1.6.7
305
-
306
- - Fix #747: the tooltip value wasn't shown because of an issue related to minimizing the code
307
- - Fix #743: the tooltip position now incorporates the scroll position
308
- - Fix drag handle styling (typo)
309
- - Make drag handle area (not the style) bigger so it's easier to grab
310
-
311
- _[Detailed changes since v1.6.6](https://github.com/higlass/higlass/compare/v1.6.6...v1.6.7)_
312
-
313
- ## v1.6.6
314
-
315
- - Fix #732: Remove the hold ALT feature as it's confusion and leads to a weird bug.
316
- - Fix leaking dark mode setting
317
- - Change option to activate dark theme from `isDarkTheme: true` to `theme: 'dark'`. Also, use `setTheme()` of the JsAPI instead of `setDarkTheme()` from now on.
318
- - Copy the tile data before mutation to fix an issue when displaying the same tileset twice (once in the upper right and lower left triangle)
319
-
320
- _[Detailed changes since v1.6.5](https://github.com/higlass/higlass/compare/v1.6.5...v1.6.6)_
321
-
322
- ## v1.6.5
323
-
324
- - Fixed the replace track bug (where replacing a center track wouldn't do anything)
325
-
326
- _[Detailed changes since v1.6.4](https://github.com/higlass/higlass/compare/v1.6.4...v1.6.5)_
327
-
328
- ## v1.6.4
329
-
330
- - Truly fix #593: zoom to data extent when adding the first track to an empty view
331
-
332
- _[Detailed changes since v1.6.3](https://github.com/higlass/higlass/compare/v1.6.3...v1.6.4)_
333
-
334
- ## v1.6.3
335
-
336
- - Dynamically update dark theme when the options change
337
- - Fix #722: added `labelShowResolution` as an option to allow hiding the `[Current data resolution...]` text
338
- - Add support for missing values (`NaN`s) to the 1D heatmap track
339
- - Use the new link format
340
-
341
- _[Detailed changes since v1.6.2](https://github.com/higlass/higlass/compare/v1.6.2...v1.6.3)_
342
-
343
- ## v1.6.2
344
-
345
- - Render `horizontal-heatmap` track properly in PIXI v4 and v5
346
- - Expose pixi renderer to plugin tracks to allow them to render textures from graphics objects. (More here: https://github.com/pixijs/pixi.js/issues/5394)
347
-
348
- _[Detailed changes since v1.6.1](https://github.com/higlass/higlass/compare/v1.6.1...v1.6.2)_
349
-
350
- ## v1.6.1
351
-
352
- - Fix visual glitches with the new Modal when run in `higlass-app`
353
- - Really fix #651: set correct namespace for SVG exports
354
- - Treat `tilesetInfo.mirror_tiles = false` as a falsy value
355
- - Fixed: `Save and Close` in the ViewConfigEditor works properly
356
-
357
- _[Detailed changes since v1.6.0](https://github.com/higlass/higlass/compare/v1.6.0...v1.6.1)_
358
-
359
- ## v1.6.0
360
-
361
- - Add an option to restrict the extent of central heatmaps to the upper-right or lower-left corner to enable comparison of two heatmaps in the center. Run `npm start` and see [http://localhost:8080/apis/svg.html?/viewconfs/diagonal-split-heatmap.json](http://localhost:8080/apis/svg.html?/viewconfs/diagonal-split-heatmap.json) for an example
362
- - Updated `pixi.js` to version `5`. In your `html` files you need to replace the previous PixiJS loader with `<script crossorigin src="https://unpkg.com/pixi.js@5/dist/pixi.min.js"></script>` (or `<script crossorigin src="https://unpkg.com/pixi.js-legacy@5/dist/pixi-legacy.min.js"></script>` if you want to use the Canvas renderer)
363
- - Add a dialog to directly edit the view config in the browser
364
- - Replace ReactBootstrap modal with custom modal to not rely on Bootstrap and support Jupyter
365
- - Updated `pub-sub-es` to version `1.2.1` to fix a bug in the shorthand event unsubscription
366
- - Added an example of a map overlay
367
- - Support semi-transparent colormaps through RGBA colors
368
- - Update Mapbox endpoint. See [http://localhost:8080/others/mapbox.html](http://localhost:8080/others/mapbox.html) for an example.
369
- - Improve performance of the `mousemove`-related event handling
370
- - Remove unused properties from the exported view config
371
- - Improve performance of tiles fetching through a combination of throttling and debouncing
372
- - Fix a minor visual glitch with the positioning of track-related `div`s
373
- - Fix OSM track to avoid CORS issues in Chrome and allow setting `minPos` to `0`
374
- - Fix #648: Auto select and copy URL when exporting a view by link
375
- - Fix #647: Shows correct URL when specifying an absolute URL as `exportViewUrl` in the viewconf
376
- - Fix #651: set correct namespace for SVG exports
377
- - Fix #593: zoom to data extent when adding the first track to an empty view
378
-
379
- _[Detailed changes since v1.5.8](https://github.com/higlass/higlass/compare/v1.5.8...v1.6.0)_
380
-
381
- ## v1.5.8
382
-
383
- - Fix a value scale syncing bug
384
- - Update the docs
385
-
386
- _[Detailed changes since v1.5.7](https://github.com/higlass/higlass/compare/v1.5.7...v1.5.8)_
387
-
388
- ## v1.5.7
389
-
390
- - Fix #637 - SVG export fill color doesn't match what is selected
391
- - Switch to nearest neighbor interpolation for horizontal heatmaps
392
-
393
- _[Detailed changes since v1.5.8](https://github.com/higlass/higlass/compare/v1.5.6...v1.5.7)_
394
-
395
- ## v1.5.6
396
-
397
- - Allow any horizontal track to also be placed on the left or right
398
-
399
- _[Detailed changes since v1.5.8](https://github.com/higlass/higlass/compare/v1.5.6...v1.5.7)_
400
-
401
- ## v1.5.5
402
-
403
- - Fixed #612: resolved an issue with caseinsensitive chromosome names
404
- - Destroy heatmap sprites and axis texts to mitigate memory leak
405
-
406
- _[Detailed changes since v1.5.4](https://github.com/higlass/higlass/compare/v1.5.4...v1.5.5)_
407
-
408
- ## v1.5.4
409
-
410
- - Fix the multiple component passive event issue by replacing the dom-event.js handlers with a class so that each component maintains its own context
411
-
412
- _[Detailed changes since v1.5.3](https://github.com/higlass/higlass/compare/v1.5.3...v1.5.4)_
413
-
414
- ## v1.5.3
415
-
416
- - Let HorizontalLineTracks look up tileset_info.tile_size
417
- and tileset_info.bins_per_dimension
418
- - Specify default track types directly in `showAvailableTrackTypes` API
419
- - Updated the docs deploy directory
420
- - Updated the javascript API example to include a full working html page
421
- - Use default height for new tracks rather than min height. Fixes
422
- newly added gene annotations so that they show names without having
423
- to be resized
424
- - Fixed bug that was causing overlay tracks to not appear
425
- - Fixed horizontal-vector-heatmap error thrown bug by padding incomplete
426
- incoming data arrays
427
-
428
- _[Detailed changes since v1.5.1](https://github.com/higlass/higlass/compare/v1.5.1...v1.5.3)_
429
-
430
- ## v1.5.1
431
-
432
- - Fixed UI hanging on mouseover of zoomed out matrix bug
433
- - Fixed #588: horizontal heatmap zoom limit bug
434
- - Reset value scale locks when new viewconf is added
435
- - Added a default track type for the chromsizes datatype
436
- - Fixed drag handler pubSub reference
437
- - Fixed #596: scrolling while zooming bug introduced in latest chrome
438
-
439
- _[Detailed changes since v1.5.0](https://github.com/higlass/higlass/compare/v1.5.0...v1.5.1)_
440
-
441
- ## v1.5.0
442
-
443
- - Allow sharing the mouse position globally. See [`docs/examples/others/global-mouse-position.html`](docs/examples/others/global-mouse-position.html) for an example.
444
- - Allow disabling the change of views and tracks separately by setting `viewEditable: false` and `tracksEditable: false` in your view config.
445
- - Added ability to define label margins. See [`docs/examples/viewconfs/label-margin.json`](docs/examples/viewconfs/label-margin.json) for an example.
446
- - Make view spacing adjustable via initialization options. See [/docs/examples/others/adjust-view-spacing.html](/docs/examples/others/adjust-view-spacing.html) for an example.
447
- - Add a new option to tracks that support axis: `axisMargin` to add some margin to an axis. See [docs/examples/viewconfs/axis-margin.json](docs/examples/viewconfs/axis-margin.json) for an example
448
- - Add a new option to BarTrack for drawing a demarcation line at the bottom of the track, i.e., at the zero value. See [`/apis/svg.html?/viewconfs/bar-zero-line.json`](/apis/svg.html?/viewconfs/bar-zero-line.json) for an example.
449
- - Fixed an issue with small offsets when exporting bar tracks to SVG
450
- - Fixed an issue where bars in a `BarTrack` related to values higher than `valueScaleMax` were not drawn.
451
- - Fixed an issue with `hgApi.setTrackValueScaleLimits`
452
- - Fix #291: allow web page scrolling when zoomFixed is set to true
453
- - Fix #578: BarTrack SVG export overplotting error.
454
- - Fix #584: Reset viewport is broken
455
-
456
- _[Detailed changes since v1.4.2](https://github.com/higlass/higlass/compare/v1.4.2...v1.5.0)_
457
-
458
- ## v1.4.2
459
-
460
- - Fix #568, #569
461
-
462
- ## v1.4.1
463
-
464
- - Allow users to choose adding the chromosome grid overlay from the Add Track Dialog when selecting a cooler file.
465
- - Expose version from hglib. E.g., `window.hglib.version`
466
-
467
- ## v1.4.0
468
-
469
- - Add `constIndicators` as an option to 1D tracks for displaying a visual indicator (e.g., a line) at a constant value.
470
- - Added `[glyph-color]` as the default option for line and bar tracks
471
- - Add new public event `cursorLocation`. See [`docs/examples/apis/cursor-location.html`](docs/examples/apis/cursor-location.html) for an example.
472
- - Extend `mouseMoveZoom` event to support 1D data tracks.
473
- - Expose D3 libraries to plugin tracks
474
- - Overlay tracks now properly allow for extent to include multiple ranges.
475
- - Overlay tracks can now optionally have extent ranges configured as a 4-tuple, separating x ranges from y ranges
476
-
477
- ## v1.3.1
478
-
479
- - Clear mouse position indicator when leaving the root dom element, on blurring the window, and when no track is hovered
480
-
481
- ## v1.3.0
482
-
483
- - Changed `defaultOptions` to `defaultTrackOptions` in the hglib.viewer options.
484
- - Added `TiledPixiTrack.on` event handler to listen to data changes
485
- - Added several API endpoints: `getComponent()`, `setAuthHeader()`, `getAuthHeader()`,
486
- - Added export of several utility functions: `waitForJsonComplete()`, `waitForTilesLoaded()`, `waitForTransitionsFinished()`, `mountHGComponent()`, `getTrackObjectFromHGC()`
487
- - Added the ability to specify default track options through the API
488
- - Added nesting to the tileset finder so that tilesets can be grouped together into categories
489
- - Added the `axisLabelFormatting` option to 1d quantitative tracks
490
- - Added TiledPixiTrack.on event handler
491
- - Added getTrackObject to exports
492
- - Added support for overlay tracks
493
- - Minor bug fix wherein valueScaleMin and valueScaleMax weren't used when set to 0
494
- - Added support for click event handling of 1D and 2D annotations from `1d-annotation` and `chromosome-2d-annotations` tracks
495
- - Cloned views split vertically first (#259)
496
- - Change component height when a new viewconf is passed in
497
- - Add a fudge factor to ensure that the entire view is shown in the grid layout
498
- - Refactored the pub-sub service to avoid implicit global event listening
499
- - Fix a minor visual glitch in the gene annotation track
500
- - Expose `mix()` from `mixwith` to plugin tracks
501
- - Support different aggregation modes (mean, min, max, std) for bigWig files
502
- - Changed `defaultOptions` to `defaultTrackOptions` in the hglib.viewer options.
503
- - Clear mouse position indicator when leaving the root dom element, on blurring the window, and when no track is hovered
504
- - Fix several issue with SVG export
505
- - Minor bug fix wherein valueScaleMin and valueScaleMax weren't used when set to 0
506
- - Fix #401
507
- - Fix #395
508
- - Fix #360
509
- - Support different aggregation modes (mean, min, max, std) for bigWig files
510
-
511
- ## v1.2.8
512
-
513
- - Added `editable` as a possible option to hglib.viewer()
514
- - Enabled arbitrary tile resolution in HeatmapTiledPixiTrack. It just needs to receive `bins_per_dimension` in the tileset info. Otherwise it defaults to 256.
515
-
516
- ## v1.2.6
517
-
518
- - Fixed trackSourceServer export
519
- - Fixed BedLikeTrack errors being thrown
520
-
521
- ## v1.2.5
522
-
523
- - Fix remote viewConf loading in HiGlassComponent
524
-
525
- ## v1.2.4
526
-
527
- - Fix #322
528
- - Fix missing update of the value scale upon rerendering
529
- - Fix absToChr and chrToAbs of the ChromInfo API
530
- - Fixed a nasty rendering bug in the chrom labels track
531
-
532
- ## v1.2.3
533
-
534
- - Fixed line inversion issue (#268)
535
- - Fixed fetched area size mismatch issue on mouseover
536
- - Added mouseover text to UI elements
537
- - Upgraded to webpack 4
538
- - Started building hglib.js and hglib.min.js
539
- - Support for searching for gene names with dashes
540
- - Sort tilesets alphabetically (#256)
541
- - Fixed zoom linking issues (#251, #76)
542
-
543
- ## v1.2.1 and v1.2.2
544
-
545
- - Accidental releases. Please ignore.
546
-
547
- ## v1.2.0
548
-
549
- - Add 1D heatmap track (#303): Alternative visual representation of 1D bigwig tracks. See https://github.com/higlass/higlass/pull/303 and https://github.com/higlass/higlass/blob/develop/docs/examples/1d-heatmap-track.html for an example.
550
-
551
- ![1D Heatmap Track](https://user-images.githubusercontent.com/932103/43858298-a7463ece-9b1b-11e8-9da4-a6fccdde2406.png '1D Heatmap Track')
552
-
553
- - Add fixing y-scale of 1D data tracks (#297). See https://github.com/higlass/higlass/pull/297 and https://github.com/higlass/higlass/blob/develop/docs/examples/api-set-track-value-scale-limits.html for an example.
554
- - Add JS-API for resetting the viewport back to the initial x and y domains in the viewconfig (#289)
555
- - Add JS-API for adjusting the margin of the HiGlass instance (#286). See https://github.com/higlass/higlass/pull/286 for an example.
556
- - Add JS-API for getting the min and max value of a track (#298). See https://github.com/higlass/higlass/blob/develop/docs/examples/api-get-min-max-value.html for an example.
557
- - Enhance bed track (#278): support value encoding as the `y` offset or `color`. See https://github.com/higlass/higlass/pull/278 for an example.
558
- - Enhance gene annotation track (#314): See https://github.com/higlass/higlass/pull/314 and https://github.com/higlass/higlass/blob/develop/docs/examples/gene-annotations.html for an example.
559
-
560
- ![Enhanced Gene Annotation Track](https://user-images.githubusercontent.com/932103/44225400-70b7f500-a15b-11e8-9656-d2ba161bccf7.png 'Enhanced Gene Annotation Track')
561
-
562
- - Enhance chrom label track (#305): add support for adjusting the font size, font alignment, and font outline to use space more economically. See https://github.com/higlass/higlass/pull/305 and https://github.com/higlass/higlass/blob/develop/docs/examples/chromosome-labels.html for an example.
563
-
564
- ![Enhanced Chrom Label Track](https://user-images.githubusercontent.com/932103/43924834-9baaf4c8-9bf3-11e8-8167-1ce1dce70849.png 'Enhanced Chrom Label Track')
565
-
566
- - Enhance bar track (#304): add color and gradient encoding plus diverging tracks. See https://github.com/higlass/higlass/pull/304 and https://github.com/higlass/higlass/blob/develop/docs/examples/bar-track-color-range.html for an example.
567
-
568
- ![Enhanced Bar Track](https://user-images.githubusercontent.com/932103/43865156-c00aa53a-9b2f-11e8-9213-bfd0af04f491.png 'Enhanced Bar Track')
569
-
570
- - Expose `absToChr` and `chrToAbs` API on `ChromInfo` (#283 and #307)
571
- - Upgrade to React `v16.5`
572
- - Removed numjs (#320)
573
- - Update tool tip appearance (#309)
574
- - Make resize handle fade out and in upon mouse enter of a draggable div
575
- - Enlarge resize handle upon mouse enter
576
- - Remove all tracks from the 'whole' window when clearing the view
577
- - Fix viewport projection issue when there are vertical and horizontal rules
578
- - Fix colorbar positioning bug
579
- - Fix #317 (moving gene positions)
580
- - Fix #263
581
- - Fix #245: track type selection bug
582
- - Fix #262: zoom to data extent issue
583
-
584
- ## v1.1.5
585
-
586
- - Merge'd Chuck's PR for adding 'same-origin' to fetch request headers
587
- - Fixed a bug where a view without a layout is created with a width of 1
588
-
589
- ## v1.1.4
590
-
591
- - Fix the checkAllTilesetInfoReceived function so that it ignores left and top
592
- axis tracks
593
- - First release to be registered with Zenodo
594
-
595
- ## v1.1.3
596
-
597
- - Add z-index to mouseover div so that it's not hidden behind other elements
598
-
599
- ## v1.1.2
600
-
601
- - Inline the SVG styles so they aren't overwritten by other elments on the
602
- page
603
- - Inline TrackControl svg styles so they aren't overwritten by page css
604
- settings
605
- - Clear gene annotation graphics before redrawing
606
-
607
- ## v1.1.1
608
-
609
- - Fixed export track data bug in heatmaps that are not combined tracks
610
-
611
- ## v1.1.0
612
-
613
- - Check whether the tileset_info specifies that the tiles should be mirrored
614
- - Added data export feature
615
- - Added showMousePosition and showMouseTooltip to horizontal-bar-track
616
-
617
- ## v1.0.4
618
-
619
- - Zoom through the viewport projection
620
-
621
- ## v1.0.3
622
-
623
- - Fixed cross rule bug
624
-
625
- ## v1.0.2
626
-
627
- - Added vertical divergent bar tracks
628
- - Fixed export in SVG
629
- - Fix mouseover error when trackrenderer hasn't been initialized yet
630
- - Added zoomFixed option to the top level of the viewconf
631
- - Use transpiled version of `mixwith.js`
632
- - Add options to change the background of the label and colorbar
633
-
634
- ## v1.0.1 (2018-06-14)
635
-
636
- - Fixed background export in SVG
637
- - Turned off line mouseover by default
638
-
639
- ## v1.0.0-alpha.12
640
-
641
- - Fixed long loading bug on zoomed in genes
642
-
643
- ## v1.0.0-alpha.11
644
-
645
- - Fixed gene stretching issues
646
-
647
- ## v1.0.0-alpha.10
648
-
649
- - Fixed background rendering after resizing
650
- - Fixed viewconf export link (use state.viewconf vs props.viewconf)
651
-
652
- ## v1.0.0-alpha.9
653
-
654
- - Fixed lock value scales
655
-
656
- ## v1.0.0-alpha.8
657
-
658
- - Fixed tooltip scrollbar appearance
659
- - Fixed context menu appearing issue
660
-
661
- ## v1.0.0-alpha.7
662
-
663
- - Fixed scrolling bug when multiple higlass components are on a single page
664
- - Fixed hover bug in combined tracks
665
-
666
- ## v1.0.0-alpha
667
-
668
- - Added triangles to genes
669
- - Preliminary authentication support
670
- - Added track for displaying gigapixel images
671
- - Added GeoJSON track and updated OSM track
672
- - Added mouseMoveZoom event to public API
673
- - Fixed and extended pubSub module
674
- - Added flexible per-track crosshair
675
- - Fixed and robustified range selection API
676
- - Display error message on error
677
- - Don't error when displaying menus when invalid track type is
678
- entered
679
- - Added an endpoint for sharing view configs as a link (`shareViewConfigAsLink()`) and exporting them as png and svg (`get('png' || 'svg')`)
680
- - Simplified `hglib` API
681
- - Updated third-party libs to get rid of deprecation warnings for React v16
682
- - Fixed small bug in placing rules
683
- - Display error when failing to retrieve tilesetInfo
684
-
685
- * Added support for cross-section tracks
686
-
687
- - Rendering improvements
688
-
689
- ## v0.10.22 (2018-02-22)
690
-
691
- - Added options to change the fill color of bedlike tracks
692
-
693
- ## v0.10.21 (2018-02-21)
694
-
695
- - Exposed the ChromosomeInfo structure as part of the hglib API
696
-
697
- ## v0.10.20 (2018-02-??
698
-
699
- - Rendering improvements
700
-
701
- ## v0.10.20 (2018-02-20)
702
-
703
- - Fixed api variable in HiGlassComponent
704
- - Fixed relToAbsChromPos so that it converts locations to numbers before
705
- adding
706
- - Added strokeWidth as an option to the viewport projection track
707
-
708
- ## v0.10.19 (2018-02-11)
709
-
710
- - Fixed the 2D chromosome labels track
711
-
712
- ## v0.10.18 (2018-02-11)
713
-
714
- - Fixed Horizontal2DTilesTrack
715
-
716
- ## v0.10.16 (2018-
717
-
718
- - Don't show the "Strange tileData" warnings
719
- - Pegged bootstrap to version 3.3.7
720
-
721
- ## v0.10.16 (2018-02-01)
722
-
723
- - Fixed a bug during active range selection when the _select_ mouse tool is deactivated
724
-
725
- ## v0.10.15 (2018-01-30)
726
-
727
- - Added the vertical bed-like track
728
-
729
- ## v0.10.13 (2018-01-25)
730
-
731
- - Added the multivec track
732
-
733
- ## v0.10.12 (2018-01-21)
734
-
735
- - Fixed pseudocounts in linear-scaled heatmaps
736
-
737
- ## v0.10.12 (2018-01-20)
738
-
739
- - Fixed get scale bug
740
-
741
- ## v0.10.11 (2018-01-17)
742
-
743
- - Fixed non-draggable views bug
744
-
745
- ## v0.10.10 (2018-01-17)
746
-
747
- - Default to log scaling if there are negative values
748
- - Fixed the custom colormap
749
- - Fix the gene annotations color changing
750
- - Fixed two regressions regarding the viewport projections
751
-
752
- ## v0.10.9 (2018-01-13)
753
-
754
- - Skipping a version because the latest version wasn't specified in
755
- package.json
756
-
757
- ## v0.10.8
758
-
759
- - Skipping a version because the latest version wasn't specified in
760
- package.json
761
-
762
- ## v0.10.7 (2018-01-13)
763
-
764
- - Show current data resolution in tiled sets containing raw resolutions rather
765
- than zoom levels
766
-
767
- ## v0.10.6 (2017-12-28)
768
-
769
- - Load ResizeSensors after the element is attached to the DOM tree
770
- - Added DivergentBarTrack
771
- - Fixed submenu hiding bug
772
-
773
- ## v0.10.5 (2017-12-27)
774
-
775
- - Fixed bug in TrackRenderer.setUpInitialScales where updating the view with
776
- new equivalent initial domains and different dimensions led to the view being
777
- misplaced
778
- - Added z-index to popup menus
779
-
780
- ## v0.10.4 (2017-12-16)
781
-
782
- - Fixed a bug in zoomToData
783
- - New API call for setViewConfig
784
- - New API call for zoomToDataExtent
785
-
786
- ## v0.10.3 (2017-12-13)
787
-
788
- - Don't include a colon if the port is 80
789
- - Added an option to clear the view
790
- - Exclude NaN values when setting the valueScale
791
- - Fixed bug related to displaying empty matrix tiles
792
-
793
- ## v0.10.2 (2017-12-12)
794
-
795
- - Fixed a bug in loading tileset info that isn't there
796
- - Better error handling on internal server error
797
- - Removed functionless menu item
798
-
799
- ## v0.10.1 (2017-12-05)
800
-
801
- - Fixed bug in Bedlike tracks that don't have a header
802
-
803
- ## v0.10.0 (2017-12-05)
804
-
805
- - Change track type from the config menu
806
- - Initial framework for divided by tracks
807
- - Y-positioned bed-like tracks
808
-
809
- ## v0.9.16 (2017-
810
-
811
- - Fixed undefined error when toggling genome position search box
812
-
813
- ## v0.9.15 (2017-11-22)
814
-
815
- - Fixed bug where newly selected annotations weren't being used
816
- - Added the hideHeader option
817
- - Added a warning for malformed gene annotations
818
- - Free up webgl renderer resources when unmount
819
- - Minor CSS cleanup
820
- - Fix resizing bug that appears after closing a view
821
- - Warn if there are no track source servers specified in the viewconf
822
-
823
- ## v0.9.14 (2017-11-11)
824
-
825
- - Show labels on bar chart
826
-
827
- ## v0.9.13 (2017-11-09)
828
-
829
- - Fixed gene position searching regression
830
-
831
- ## v0.9.12 (2017-11-08)
832
-
833
- - Fix inter-chromosomal searches (chr1-chr2)
834
-
835
- ## v0.9.11 (2017-11-08)
836
-
837
- - Fix gene annotation coloring bug
838
- - Fix menu clash error that occurs when a center track is specified
839
- without a combined track
840
- - Zoom into entire chromosomes by just entering its name
841
-
842
- ## v0.9.10 (2017-11-01)
843
-
844
- - Fixed d3 brush Error: <rect> attribute height: Expected length, "Infinity"
845
- - Fixed scale initialization error
846
- - Added back heatmap value scaling
847
- - Fixed horizontal heatmap multires tile loading
848
- - Better point export
849
-
850
- ## v0.9.9 (2017-11-01)
851
-
852
- - Fix SVG bar chart export
853
- - Fixed network error on SVG export again (from v0.8.44)
854
-
855
- ## v0.9.8 (2017-10-31)
856
-
857
- - Switch back to minified build
858
-
859
- ## v0.9.7 (2017-10-31)
860
-
861
- - Initialize scales when viewconfig is loaded rather than on
862
- handleScalesChanged
863
-
864
- ## v0.9.6 (2017-10-31)
865
-
866
- - Faulty build (package.json wasn't there)
867
-
868
- ## v0.9.5 (2017-10-31)
869
-
870
- - Fix visual clash of the center track's context menu and the colormap
871
- - Make visualization of 2D annotations more flexible: stroke width and fill / stroke opacity can be changed
872
- - Create debug output files
873
-
874
- ## v0.9.4 (2017-10-26)
875
-
876
- - Reintroduced value scale serialization fix
877
- - Fixed HorizontalHeatmapExport
878
- - Added a minimum width to 2D annotations
879
- - Added SVG export for 2d-rectangle-domains track
880
-
881
- ## v0.9.3 (2017-10-23)
882
-
883
- - Removed console log statement
884
-
885
- ## v0.9.2 (2017-10-23)
886
-
887
- - Fixed the build script to copy hglib.css rather than style.css
888
-
889
- ## v0.9.1 (2017-10-23)
890
-
891
- - Add support for vertical bar tracks
892
- - Fixed .travis.yml release issue
893
-
894
- ## v0.9.0 (2017-10-21)
895
-
896
- - Add 1D and 2D range selection
897
- - Add support for SASS
898
- - Add support for CSS Modules
899
- - Update visuals of the context menu and view header
900
- - Integrate search bar into view header
901
- - Add ESLint and adhere to consistent code style
902
- - (Fix #135) - Colorbar moves with the track when it's being resized
903
- - (Fix #126) - Gene annotations shouldn't overlap on vertical tracks anymore
904
- - Keep track controls visible if config menu is active
905
- - Show child menus above the parent if there isn't enough space on the bottom
906
- - Add port number when exporting viewconfs from a non-standard port
907
- - Support arbitrary resolutions in heatmaps
908
-
909
- ## v0.8.44
910
-
911
- - Redraw TiledPixiTracks after the tileset info has been received
912
- - Remove value scale locks on handleCloseTrack
913
- - Check that tiledPlot is defined in createSVG to fix the export
914
- failing when there's two side-by-side by views created after closing
915
- one
916
- - Fixed the "Failed: network error" issue in chrome by changing the
917
- "download" function in utils.js
918
-
919
- ## v0.8.43
920
-
921
- - More fixes for SVG output for bedlike tracks
922
-
923
- ## v0.8.42
924
-
925
- - Fixed SVG output for bedlike tracks
926
-
927
- ## v0.8.41
928
-
929
- - Fixed chromosome grid color bug
930
- - Fixed chromosome grid loading with many values bug
931
-
932
- ## v0.8.40
933
-
934
- - Fixed value scale locking bug
935
-
936
- ## v0.8.37
937
-
938
- - Fixed center track label background oddness (#144)
939
-
940
- ## v0.8.36
941
-
942
- - (fix #146) Fixed value scale locking serialization bug
943
- - Fixed gene annotation SVG export
944
- - Fixed chromosome ticks SVG export
945
-
946
- ## v0.8.35
947
-
948
- - Fixed colorbar hiding bug (Issue #131)
949
-
950
- ## v0.8.34
951
-
952
- - Fixed horizontal heatmap loading after the adjustable color scale changes
953
- - Fixed vertical heatmap loading
954
- - Fixed vertical heatmap colorscale brush in LeftTrackModifier
955
-
956
- ## v0.8.33
957
-
958
- - Removed the outside colorbar labels option (it's a little
959
- ambiguous on the right side since the labels will be adjacent
960
- to the other axis elements.
961
-
962
- ## v0.8.32
963
-
964
- - Removed tests from package.json so that build completes (tests fail on
965
- travis for some reason)
966
-
967
- ## v0.8.31
968
-
969
- - Add a color limit selection to the Heatmap track in HiGlass
970
-
971
- ## v0.8.30
972
-
973
- - Cherry picked the BedLikeTrack from the circle branch
974
-
975
- ## v0.8.28
976
-
977
- - Fixed dependencies (peer and normal)
978
- - Fixed other minor issues with `package.json`
979
-
980
- ## v0.8.27
981
-
982
- - Fixed bug wher the "Loading" sign remained with 1D point tracks
983
-
984
- ## v0.8.26
985
-
986
- - Different mapbox style options
987
-
988
- ## v0.8.25
989
-
990
- - Hidden OSM tiles
991
- - Customizeable osm width
992
-
993
- ## v0.8.24
994
-
995
- - Major performance improvements for Gene annotations and horizontal points
996
- - Fixed bug in searching for genome positions with a space at one of the ends
997
- - Added the OSM tiles
998
-
999
- ## v0.8.23
1000
-
1001
- - Don't show chromosome sizes as a separate track
1002
-
1003
- ## v0.8.22 - 2017-07-13
1004
-
1005
- - Safari add track bug fix
1006
- - Backwards compatibility on selectable chromosome axis tracks
1007
-
1008
- ## v0.8.21 - 2017-07-10
1009
-
1010
- - Fixed the default transformation for horizontal tracks
1011
-
1012
- ## v0.8.20 - 2017-07-10
1013
-
1014
- - Fix label display
1015
-
1016
- ## v0.8.19 - 2017-07-10
1017
-
1018
- - Added the ability to select different transformations
1019
-
1020
- ## v0.8.18 - 2017-06-29
1021
-
1022
- - Fixed custom colormap picker
1023
- - Fixed overlayed track addition on double click
1024
-
1025
- ## v0.8.17 - 2017-06-28
1026
-
1027
- - Performance improvements
1028
-
1029
- ## v0.8.16 - 2017-06-27
1030
-
1031
- - Fixed a regression where closing views didn't remove the associated PIXI
1032
- Components
1033
- - Increased the drag timeout time to 5 seconds
1034
-
1035
- ## v0.8.15 - 2017-06-26
1036
-
1037
- - Lowered the maximum number of tiles retrieved at once to 20
1038
-
1039
- ## v0.8.14 - 2017-06-26
1040
-
1041
- - Increase the maximum number of tiles retrieved at once to 40
1042
-
1043
- ## v0.8.13 - 2017-06-26
1044
-
1045
- - Option to draw borders around tracks
1046
- - Option to change the stroke, fill colors and opacity of the
1047
- horizontal-2d-rectangle-domains track
1048
-
1049
- ## v0.8.12 - 2017-06-26
1050
-
1051
- - Hide overflow track handles
1052
-
1053
- ## v0.8.11 - 2017-06-26
1054
-
1055
- - Fixed double click track addition bug
1056
- - Mask view boundaries so that when the tracks are too large
1057
- to fit inside, they don't overflow outside of their view
1058
- - Added favicon
1059
-
1060
- ## v0.8.10 - 2017-06-25
1061
-
1062
- - Multiple tileset selection
1063
- - Disabled zooming on scrolling fix
1064
-
1065
- ## v0.8.9
1066
-
1067
- - Make sure that the zoomable div matches the size of the container
1068
-
1069
- ## v0.8.8 - 2017-06-20
1070
-
1071
- - Don't start zooming when scrolling into a HGC
1072
-
1073
- ## v0.8.7 - 2017-06-18
1074
-
1075
- - Decreased the maximum colorbar height
1076
- - Made the draggable div handles more transparent
1077
- - Lowered the minimum height for chromosome axes
1078
-
1079
- ## v0.8.6 - 2017-06-18
1080
-
1081
- - Fixed a bug where the HG Component would automatically and indefinitely
1082
- increase in size
1083
-
1084
- ## v0.8.5 - 2017-06-16
1085
-
1086
- - Fixed view linking bug (regression)
1087
- - Added horizontal and vertical 2D domains tracks
1088
-
1089
- ## v0.8.4 - 2017-06-12
1090
-
1091
- - Include a limit in the tilesets query so that all results are returned
1092
-
1093
- ## v0.8.3 - 2017-06-06
1094
-
1095
- - Fixed a regression where adding new tracks doesn't work
1096
-
1097
- ## v0.8.2 - 2017-06-01
1098
-
1099
- - Move hglib.css to dist/styles rather than dist/
1100
-
1101
- ## v0.8.1 - 2017-06-01
1102
-
1103
- - Changed package.json to create hglib.css rather than style.css
1104
-
1105
- ## v0.8.0 - 2017-06-01
1106
-
1107
- - Switched to webpack 2
1108
- - Various warning fixes in the code
1109
- - Pull chromsizes from the tilesets table instead
1110
- - Remove the chroms table and app
1111
-
1112
- ## v0.7.3 - 2017-05-23
1113
-
1114
- - Added stroke width as a property of line tracks
1115
- - Fixed view layout bug caused by the "i" member of the layout not
1116
- matching the view's uid
1117
- - Fixed resizing so that vertical changes get handled immediately
1118
-
1119
- ## v0.7.2
1120
-
1121
- - Added purple and turquoise colors
1122
- - Added an option to control the label opacity
1123
-
1124
- ## v0.7.1
1125
-
1126
- - Added horizontal and vertical track viewport projections
1127
- - Bug fix where assembly name gets removed from track label
1128
-
1129
- ## v0.7.0
1130
-
1131
- - Added an assembly selector to the GenomePositionSearchBox
1132
- - Prefix track names with their assembly
1133
-
1134
- ## v0.6.9
1135
-
1136
- - Lower the default resolution of lines for performance reasons
1137
- - Added outsideLeft, outsideRight, outsideTop and outsideBottom
1138
- as available axis positions
1139
-
1140
- ## v0.6.8
1141
-
1142
- - Component sizes are adjsuted on component load
1143
- - Genome position search box styling is set to not
1144
- have a bottom margin
1145
-
1146
- ## v0.6.7
1147
-
1148
- - Unbounded functionality to increase the size of the layout if new tracks are
1149
- added which increase its size
1150
- - Configurable track label background opacity
1151
- - Fixed: vertical colorbar label mirroring
1152
-
1153
- ## v0.6.6
1154
-
1155
- - Bug fix: closing a track which had a value scale lock with another track now
1156
- works
1157
-
1158
- ## v0.6.5
1159
-
1160
- - Bug fix: tracks rendered with locked scale, rather than just the colorbar
1161
- - Bug fix: locked line scales
1162
- - Bug fix: assorted other track locking, scale and colorbar bugs
1163
-
1164
- ## v0.6.4
1165
-
1166
- - Added value scale locking
1167
- - Fixed bug where newly added heatmaps didn't render (syncTrackObjects needs
1168
- to call applyZoomTransform)
1169
- - Fixed bug where new chromosome axis didn't appear after being added - Had to call animate after the chromosome info was received
1170
-
1171
- ## v0.6.3
1172
-
1173
- - Added colorbar for Heatmaps
1174
- - Draw scales on the outside of the linear tracks
1175
- - Added the SquareMarkerTrack
1176
-
1177
- ## v0.6.2
1178
-
1179
- - Scale tracks from minimum to maximum value, rather than starting at 0
1180
-
1181
- ## v0.6.1
1182
-
1183
- - Fixed a minor issue with chromosome labels not being exported
1184
-
1185
- ## v0.6.0
1186
-
1187
- - Automatically draw the 2D grid after the data is loaded
1188
- - Add animated zoom transitions
1189
- - Add public BEDPE-like API to navigate to a given location
1190
- - SVG export
1191
- - Testing using Karma
1192
- - (Might have been in a different release) Default to interpolation-less rendering
1193
-
1194
- ## v0.5.16
1195
-
1196
- - Fixed resizing bug
1197
-
1198
- ## v0.5.15
1199
-
1200
- - Added mm9 chromosome labels
1201
- - Draw chromosome labels on reload
1202
- - Take name from track options
1203
-
1204
- ## v0.5.14
1205
-
1206
- - Revert the initialXDomain changes Fritz introduced because they were causing
1207
- issues with faithful reproduction of viewconfs
1208
- - Change 'tilesetInfo not loaded message' to 'loading...' until we either get
1209
- an error or the tileset is loaded
1210
- - Omit certain fields from JSON export (HiGlassComponenent.getViewsAsString)
1211
-
1212
- ## v0.5.12
1213
-
1214
- - Fixed export viewconfig link bug
1215
-
1216
- ## v0.5.11
1217
-
1218
- - Added the fall colormap and made it the default
1219
-
1220
- ## v0.5.10
1221
-
1222
- - Fix Chromosome2DAnnotations not being drawn by calling draw after the
1223
- ChromosomeInfo is loaded
1224
- - Zoom to the currently visible data
1225
- - Use the minimum position to load data that is not located at the origin
1226
- - Viewconf downloads work on Firefox
1227
- - Alert when trying to project a viewport on the same view
1228
- - Resize handle positions fixed in Firefox
1229
- - Track config button icons fixed in Firefox
1230
- - Only redraw in timedUpdate if track positions have changed
1231
- - Fixed top and left axis not appearing bug
1232
- - Fixed chromosome horizontal labels not appearing
1233
- - Show minValue pixels by scaling from minValue to maxValue + minValue and
1234
- adding minValue to each pixel
1235
- - Fix viewport projection error when new viewconfig is passed
1236
-
1237
- ## v0.5.9
1238
-
1239
- - Labels outside of the bounds of a track
1240
- - Label colors
1241
-
1242
- ## v0.5.8
1243
-
1244
- - A host of performance improvements
1245
-
1246
- ## v0.5.7
1247
-
1248
- - Empty accidental release
1249
-
1250
- ## v0.5.6
1251
-
1252
- - Add log scaling to line tracks
1253
- - Add colors to line tracks
1254
- - Add width option to 2D grid
1255
- - Add color option to 2D grid
1256
-
1257
- ## v0.5.5
1258
-
1259
- - Add per-view `zoomFixed` settings
1260
- - Added configurable viewport projection colors (projectionFillColor,
1261
- projectionStrokeColor)
1262
- - Added an empty .npmignore to prevent it from excluding the dist/
1263
- directory specified in the .gitignore
1264
- - Enhance 2D annotations by supporting RGBA, fill and stroke-dependent coloring,
1265
- and locus-wise min width / height definitions
1266
- - Remove builds. Use NPM
1267
-
1268
- ## v0.5.4
1269
-
1270
- - Fixed bug related to the selection of the plot type
1271
- - Update existing tracks before adding new ones in syncTrackObjects
1272
- - Removed the "Move up" menu item
1273
- - Deep copy incoming viewconfs so that changing them outside of the component
1274
- leads to an update
1275
- - Added onLocationChanged event listener
1276
-
1277
- ## v0.5.3
1278
-
1279
- - Forgot to bump the version number in 0.5.2
1280
-
1281
- ## v0.5.2
1282
-
1283
- - Don't draw data that extends beyond the end of the assembly
1284
- - Fixed bug where data was being hidden in empty (all 0) tiles - Changed minVisibleValue and maxVisibleValue in TiledPixiTrack
1285
- - Label the horizontal and vertical line tracks by default
1286
-
1287
- ## v0.5.1
1288
-
1289
- - Configurable gene annotation colors
1290
- - Added chromosome annotations tracks for programmatically addeable
1291
- annotations
1292
- - Fixed the 'Cannot read property 0 of undefined' bug when tileset info is
1293
- inaccessible
1294
- - Remove track resize handles when the component isn't editable
1295
- - Fix bug associated with setting a new initial[X/Y]Domain where the
1296
- cumulativeCenterOffset wasn't being reset
1297
- - Bug fix where if a view doesn't have a uid we should assign it one
1298
-
1299
- ## v0.5.0
1300
-
1301
- - Default to 12 columns
1302
- - Display a warning if tileset info isn't found
1303
- - Use 16bit floats for heatmap data
1304
-
1305
- ## v0.4.40
1306
-
1307
- - Remove default colormap from viewconfig
1308
-
1309
- ## v0.4.39
1310
-
1311
- - Switch cog and close buttons
1312
-
1313
- ## v0.4.33
1314
-
1315
- - New header colors
1316
-
1317
- ## v0.4.32
1318
-
1319
- - Reduced the number of tiles requested by the horizontal heatmap track
1320
- - Removed console log statements
1321
-
1322
- ## v0.4.31
1323
-
1324
- - Fixed regression and compatibility change with new zoom and location locking
1325
- - Fixed regression in the selection dragging
1326
-
1327
- ## v0.4.30
1328
-
1329
- - Added a minimum width to left-axis so that it doesn't only show the last two
1330
- digits by default
1331
-
1332
- * Added horizontal and vertical heatmaps
1333
-
1334
- - Styling changes for the Configure track controls
1335
- - Fixed the bug with AddTrackMenu cancel button turning black by properly
1336
- increasing the number of visible tilesets in TilesetFinder
1337
- - Added options to allow flipping horizontal and vertical charts
1338
- - Fixed NaN prefix bug
1339
- - Fixed invalid negative value attributes for <rect> bug
1340
-
1341
- ## v0.4.29
1342
-
1343
- - Moved default heatmap information to lower right hand corner
1344
- - Fixed a bug which distorted the view when initialized with an initial X
1345
- scale and Y scale
1346
- - Added white to red, white to green and white to blue scales
1347
- - Added axes for the 1D tracks
1348
- - Took the ID out of the view header
1349
- - Added a white border behind the track controls
1350
-
1351
- ## v0.4.28
1352
-
1353
- - Fixed critical regression where track replacement wasn't working because
1354
- newly created tracks didn't have their options set
1355
- - Fixed a regression where track movement wasn't working because TiledPlot
1356
- wasn't being updated
1357
- - Increase the size of the tileset selector
1358
-
1359
- ## v0.4.27
1360
-
1361
- - Changed config.js Chromosome Labels to Chromosome Axis
1362
- - Fixed default option setting so that it doesn't override provided options
1363
- - Adding zoom limit option to heatmap
1364
- - Add current resolution to the track label
1365
- - Fixed regression caused by "Fast redraw by tiling commit"
1366
- - Hitting enter in the genome position search box initiates a search
1367
-
1368
- ## v0.4.26
1369
-
1370
- - Fixed close button
1371
-
1372
- ## v0.4.25
1373
-
1374
- - Fractional zoom lock
1375
- - Faster config menu loading
1376
- - Faster track addition by limiting the udpates of TiledPlot (using
1377
- shouldComponentUpdate)
1378
-
1379
- ## v0.4.21
1380
-
1381
- - Chromosome grid positions start at position 1
1382
- - Export link includes 'app'
1383
-
1384
- ## v0.4.20
1385
-
1386
- - Changed tile API location to use included server value rather than
1387
- prepending '//'
1388
-
1389
- ## v0.4.19
1390
-
1391
- - Removed dist directory from .gitignore
1392
-
1393
- ## v0.4.18
1394
-
1395
- - Use production react in the build
1396
- - Added dist to .gitignore
1397
-
1398
- ## v0.4.17
1399
-
1400
- - Updated default view config
1401
- - Wider ticks
1402
-
1403
- ## v0.4.16
1404
-
1405
- - Fritz's public API
1406
-
1407
- ## v0.4.15
1408
-
1409
- - Fritz's lazy animation
1410
- - Fritz's public API
1411
- - Minimum height for tracks can be specified in track type definition in
1412
- config.js
1413
- - New chromosome 2D grid (for hg19)
1414
- - New chromosome 1D axis (for hg19)
1415
- - New chromosome horizontal axis (for hg19)