@jbrowse/plugin-linear-genome-view 2.6.3 → 2.7.1

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 (121) hide show
  1. package/dist/BaseLinearDisplay/components/LinearBlocks.d.ts +4 -14
  2. package/dist/BaseLinearDisplay/components/LinearBlocks.js +5 -6
  3. package/dist/BaseLinearDisplay/components/Tooltip.js +1 -1
  4. package/dist/BaseLinearDisplay/models/util.d.ts +2 -6
  5. package/dist/LinearBasicDisplay/components/SetMaxHeight.d.ts +4 -5
  6. package/dist/LinearBasicDisplay/components/SetMaxHeight.js +3 -3
  7. package/dist/LinearBasicDisplay/model.d.ts +3 -1
  8. package/dist/LinearGenomeView/components/CenterLine.d.ts +3 -4
  9. package/dist/LinearGenomeView/components/CenterLine.js +3 -3
  10. package/dist/LinearGenomeView/components/Cytobands.d.ts +6 -2
  11. package/dist/LinearGenomeView/components/Cytobands.js +37 -38
  12. package/dist/LinearGenomeView/components/GetSequenceDialog.d.ts +3 -4
  13. package/dist/LinearGenomeView/components/GetSequenceDialog.js +3 -3
  14. package/dist/LinearGenomeView/components/Gridlines.d.ts +3 -4
  15. package/dist/LinearGenomeView/components/Gridlines.js +21 -18
  16. package/dist/LinearGenomeView/components/ImportForm.d.ts +2 -2
  17. package/dist/LinearGenomeView/components/ImportForm.js +2 -1
  18. package/dist/LinearGenomeView/components/LinearGenomeView.js +19 -1
  19. package/dist/LinearGenomeView/components/MiniControls.js +13 -5
  20. package/dist/LinearGenomeView/components/OverviewRubberband.d.ts +2 -2
  21. package/dist/LinearGenomeView/components/OverviewRubberband.js +2 -1
  22. package/dist/LinearGenomeView/components/OverviewScalebar.d.ts +2 -2
  23. package/dist/LinearGenomeView/components/OverviewScalebar.js +41 -13
  24. package/dist/LinearGenomeView/components/RefNameAutocomplete/index.d.ts +2 -2
  25. package/dist/LinearGenomeView/components/RefNameAutocomplete/index.js +2 -1
  26. package/dist/LinearGenomeView/components/RefNameAutocomplete/util.d.ts +1 -3
  27. package/dist/LinearGenomeView/components/Rubberband.d.ts +4 -5
  28. package/dist/LinearGenomeView/components/Rubberband.js +3 -3
  29. package/dist/LinearGenomeView/components/Scalebar.d.ts +2 -2
  30. package/dist/LinearGenomeView/components/Scalebar.js +29 -24
  31. package/dist/LinearGenomeView/components/SearchBox.d.ts +4 -5
  32. package/dist/LinearGenomeView/components/SearchBox.js +3 -3
  33. package/dist/LinearGenomeView/components/SequenceSearchDialog.d.ts +4 -5
  34. package/dist/LinearGenomeView/components/SequenceSearchDialog.js +20 -18
  35. package/dist/LinearGenomeView/components/TrackContainer.d.ts +2 -2
  36. package/dist/LinearGenomeView/components/TrackContainer.js +2 -1
  37. package/dist/LinearGenomeView/components/TrackLabel.d.ts +2 -2
  38. package/dist/LinearGenomeView/components/TrackLabel.js +5 -21
  39. package/dist/LinearGenomeView/components/TrackLabelDragHandle.d.ts +9 -0
  40. package/dist/LinearGenomeView/components/TrackLabelDragHandle.js +32 -0
  41. package/dist/LinearGenomeView/components/TrackRenderingContainer.d.ts +2 -2
  42. package/dist/LinearGenomeView/components/TrackRenderingContainer.js +2 -1
  43. package/dist/LinearGenomeView/components/TracksContainer.d.ts +2 -2
  44. package/dist/LinearGenomeView/components/TracksContainer.js +2 -1
  45. package/dist/LinearGenomeView/components/VerticalGuide.d.ts +3 -4
  46. package/dist/LinearGenomeView/components/VerticalGuide.js +3 -3
  47. package/dist/LinearGenomeView/components/ZoomControls.d.ts +3 -4
  48. package/dist/LinearGenomeView/components/ZoomControls.js +3 -3
  49. package/dist/LinearGenomeView/components/util.d.ts +1 -1
  50. package/dist/LinearGenomeView/index.d.ts +1 -2
  51. package/dist/LinearGenomeView/index.js +3 -2
  52. package/dist/LinearGenomeView/model.d.ts +6 -6
  53. package/dist/LinearGenomeView/model.js +33 -0
  54. package/dist/LinearGenomeView/svgcomponents/SVGBackground.js +2 -2
  55. package/dist/LinearGenomeView/svgcomponents/SVGHeader.js +1 -4
  56. package/dist/LinearGenomeView/svgcomponents/SVGLinearGenomeView.js +1 -0
  57. package/dist/LinearGenomeView/svgcomponents/SVGRuler.js +2 -3
  58. package/dist/LinearGenomeView/svgcomponents/SVGScalebar.js +1 -2
  59. package/dist/LinearGenomeView/svgcomponents/SVGTrackLabel.js +3 -1
  60. package/dist/index.d.ts +37 -37
  61. package/esm/BaseLinearDisplay/components/LinearBlocks.d.ts +4 -14
  62. package/esm/BaseLinearDisplay/components/LinearBlocks.js +5 -5
  63. package/esm/BaseLinearDisplay/components/Tooltip.js +1 -1
  64. package/esm/BaseLinearDisplay/models/util.d.ts +2 -6
  65. package/esm/LinearBasicDisplay/components/SetMaxHeight.d.ts +4 -5
  66. package/esm/LinearBasicDisplay/components/SetMaxHeight.js +3 -3
  67. package/esm/LinearBasicDisplay/model.d.ts +3 -1
  68. package/esm/LinearGenomeView/components/CenterLine.d.ts +3 -4
  69. package/esm/LinearGenomeView/components/CenterLine.js +3 -3
  70. package/esm/LinearGenomeView/components/Cytobands.d.ts +6 -2
  71. package/esm/LinearGenomeView/components/Cytobands.js +37 -38
  72. package/esm/LinearGenomeView/components/GetSequenceDialog.d.ts +3 -4
  73. package/esm/LinearGenomeView/components/GetSequenceDialog.js +3 -3
  74. package/esm/LinearGenomeView/components/Gridlines.d.ts +3 -4
  75. package/esm/LinearGenomeView/components/Gridlines.js +21 -18
  76. package/esm/LinearGenomeView/components/ImportForm.d.ts +2 -2
  77. package/esm/LinearGenomeView/components/ImportForm.js +2 -1
  78. package/esm/LinearGenomeView/components/LinearGenomeView.js +20 -2
  79. package/esm/LinearGenomeView/components/MiniControls.js +13 -5
  80. package/esm/LinearGenomeView/components/OverviewRubberband.d.ts +2 -2
  81. package/esm/LinearGenomeView/components/OverviewRubberband.js +2 -1
  82. package/esm/LinearGenomeView/components/OverviewScalebar.d.ts +2 -2
  83. package/esm/LinearGenomeView/components/OverviewScalebar.js +18 -13
  84. package/esm/LinearGenomeView/components/RefNameAutocomplete/index.d.ts +2 -2
  85. package/esm/LinearGenomeView/components/RefNameAutocomplete/index.js +2 -1
  86. package/esm/LinearGenomeView/components/RefNameAutocomplete/util.d.ts +1 -3
  87. package/esm/LinearGenomeView/components/Rubberband.d.ts +4 -5
  88. package/esm/LinearGenomeView/components/Rubberband.js +3 -3
  89. package/esm/LinearGenomeView/components/Scalebar.d.ts +2 -2
  90. package/esm/LinearGenomeView/components/Scalebar.js +29 -24
  91. package/esm/LinearGenomeView/components/SearchBox.d.ts +4 -5
  92. package/esm/LinearGenomeView/components/SearchBox.js +3 -3
  93. package/esm/LinearGenomeView/components/SequenceSearchDialog.d.ts +4 -5
  94. package/esm/LinearGenomeView/components/SequenceSearchDialog.js +21 -19
  95. package/esm/LinearGenomeView/components/TrackContainer.d.ts +2 -2
  96. package/esm/LinearGenomeView/components/TrackContainer.js +2 -1
  97. package/esm/LinearGenomeView/components/TrackLabel.d.ts +2 -2
  98. package/esm/LinearGenomeView/components/TrackLabel.js +5 -21
  99. package/esm/LinearGenomeView/components/TrackLabelDragHandle.d.ts +9 -0
  100. package/esm/LinearGenomeView/components/TrackLabelDragHandle.js +27 -0
  101. package/esm/LinearGenomeView/components/TrackRenderingContainer.d.ts +2 -2
  102. package/esm/LinearGenomeView/components/TrackRenderingContainer.js +2 -1
  103. package/esm/LinearGenomeView/components/TracksContainer.d.ts +2 -2
  104. package/esm/LinearGenomeView/components/TracksContainer.js +2 -1
  105. package/esm/LinearGenomeView/components/VerticalGuide.d.ts +3 -4
  106. package/esm/LinearGenomeView/components/VerticalGuide.js +3 -3
  107. package/esm/LinearGenomeView/components/ZoomControls.d.ts +3 -4
  108. package/esm/LinearGenomeView/components/ZoomControls.js +3 -3
  109. package/esm/LinearGenomeView/components/util.d.ts +1 -1
  110. package/esm/LinearGenomeView/index.d.ts +1 -2
  111. package/esm/LinearGenomeView/index.js +2 -2
  112. package/esm/LinearGenomeView/model.d.ts +6 -6
  113. package/esm/LinearGenomeView/model.js +33 -0
  114. package/esm/LinearGenomeView/svgcomponents/SVGBackground.js +2 -2
  115. package/esm/LinearGenomeView/svgcomponents/SVGHeader.js +2 -5
  116. package/esm/LinearGenomeView/svgcomponents/SVGLinearGenomeView.js +1 -0
  117. package/esm/LinearGenomeView/svgcomponents/SVGRuler.js +3 -4
  118. package/esm/LinearGenomeView/svgcomponents/SVGScalebar.js +2 -3
  119. package/esm/LinearGenomeView/svgcomponents/SVGTrackLabel.js +3 -1
  120. package/esm/index.d.ts +37 -37
  121. package/package.json +4 -5
@@ -4,13 +4,13 @@ import { Dialog } from '@jbrowse/core/ui';
4
4
  import { getSnapshot } from 'mobx-state-tree';
5
5
  import { makeStyles } from 'tss-react/mui';
6
6
  import { observer } from 'mobx-react';
7
- import { getSession } from '@jbrowse/core/util';
7
+ import { getSession, isSessionWithAddTracks } from '@jbrowse/core/util';
8
8
  const useStyles = makeStyles()({
9
9
  dialogContent: {
10
10
  width: '40em',
11
11
  },
12
12
  });
13
- function SequenceDialog({ model, handleClose, }) {
13
+ const SequenceSearchDialog = observer(function ({ model, handleClose, }) {
14
14
  const { classes } = useStyles();
15
15
  const [value, setValue] = useState('');
16
16
  const [searchForward, setSearchForward] = useState(true);
@@ -40,24 +40,26 @@ function SequenceDialog({ model, handleClose, }) {
40
40
  const session = getSession(model);
41
41
  const { assemblyManager } = session;
42
42
  const assemblyName = model.assemblyNames[0];
43
- session.addTrackConf({
44
- trackId,
45
- name: `Sequence search ${value}`,
46
- assemblyNames: [assemblyName],
47
- type: 'FeatureTrack',
48
- adapter: {
49
- type: 'SequenceSearchAdapter',
50
- search: value,
51
- searchForward,
52
- searchReverse,
53
- caseInsensitive,
54
- sequenceAdapter: getSnapshot((_a = assemblyManager.get(assemblyName)) === null || _a === void 0 ? void 0 : _a.configuration.sequence.adapter),
55
- },
56
- });
57
- model.toggleTrack(trackId);
43
+ if (isSessionWithAddTracks(session)) {
44
+ session.addTrackConf({
45
+ trackId,
46
+ name: `Sequence search ${value}`,
47
+ assemblyNames: [assemblyName],
48
+ type: 'FeatureTrack',
49
+ adapter: {
50
+ type: 'SequenceSearchAdapter',
51
+ search: value,
52
+ searchForward,
53
+ searchReverse,
54
+ caseInsensitive,
55
+ sequenceAdapter: getSnapshot((_a = assemblyManager.get(assemblyName)) === null || _a === void 0 ? void 0 : _a.configuration.sequence.adapter),
56
+ },
57
+ });
58
+ model.showTrack(trackId);
59
+ }
58
60
  }
59
61
  handleClose();
60
62
  }, variant: "contained", color: "primary" }, "Submit"),
61
63
  React.createElement(Button, { onClick: () => handleClose(), variant: "contained", color: "secondary" }, "Close"))));
62
- }
63
- export default observer(SequenceDialog);
64
+ });
65
+ export default SequenceSearchDialog;
@@ -2,8 +2,8 @@ import React from 'react';
2
2
  import { BaseTrackModel } from '@jbrowse/core/pluggableElementTypes/models';
3
3
  import { LinearGenomeViewModel } from '..';
4
4
  type LGV = LinearGenomeViewModel;
5
- declare const _default: ({ model, track, }: {
5
+ declare const TrackContainer: ({ model, track, }: {
6
6
  model: LGV;
7
7
  track: BaseTrackModel;
8
8
  }) => React.JSX.Element;
9
- export default _default;
9
+ export default TrackContainer;
@@ -27,7 +27,7 @@ const useStyles = makeStyles()({
27
27
  zIndex: 3,
28
28
  },
29
29
  });
30
- export default observer(function TrackContainer({ model, track, }) {
30
+ const TrackContainer = observer(function ({ model, track, }) {
31
31
  const { classes } = useStyles();
32
32
  const display = track.displays[0];
33
33
  const { draggingTrackId } = model;
@@ -54,3 +54,4 @@ export default observer(function TrackContainer({ model, track, }) {
54
54
  }, onDragEnter: debouncedOnDragEnter }),
55
55
  React.createElement(ResizeHandle, { onDrag: display.resizeHeight, className: classes.resizeHandle })));
56
56
  });
57
+ export default TrackContainer;
@@ -4,5 +4,5 @@ interface Props {
4
4
  track: BaseTrackModel;
5
5
  className?: string;
6
6
  }
7
- declare const _default: React.ForwardRefExoticComponent<Props & React.RefAttributes<HTMLDivElement>>;
8
- export default _default;
7
+ declare const TrackLabel: React.ForwardRefExoticComponent<Props & React.RefAttributes<HTMLDivElement>>;
8
+ export default TrackLabel;
@@ -9,10 +9,10 @@ import { SanitizedHTML } from '@jbrowse/core/ui';
9
9
  import CascadingMenuButton from '@jbrowse/core/ui/CascadingMenuButton';
10
10
  // icons
11
11
  import MoreVertIcon from '@mui/icons-material/MoreVert';
12
- import DragIcon from '@mui/icons-material/DragIndicator';
13
12
  import CloseIcon from '@mui/icons-material/Close';
14
13
  import MinimizeIcon from '@mui/icons-material/Minimize';
15
14
  import AddIcon from '@mui/icons-material/Add';
15
+ import TrackLabelDragHandle from './TrackLabelDragHandle';
16
16
  const useStyles = makeStyles()(theme => ({
17
17
  root: {
18
18
  background: alpha(theme.palette.background.paper, 0.8),
@@ -29,19 +29,11 @@ const useStyles = makeStyles()(theme => ({
29
29
  fontSize: '0.8rem',
30
30
  pointerEvents: 'none',
31
31
  },
32
- dragHandle: {
33
- cursor: 'grab',
34
- },
35
- dragHandleIcon: {
36
- display: 'inline-block',
37
- verticalAlign: 'middle',
38
- pointerEvents: 'none',
39
- },
40
32
  iconButton: {
41
33
  padding: theme.spacing(1),
42
34
  },
43
35
  }));
44
- const TrackLabel = React.forwardRef(function ({ track, className }, ref) {
36
+ const TrackLabel = observer(React.forwardRef(function TrackLabel2({ track, className }, ref) {
45
37
  var _a;
46
38
  const { classes, cx } = useStyles();
47
39
  const view = getContainingView(track);
@@ -60,15 +52,7 @@ const TrackLabel = React.forwardRef(function ({ track, className }, ref) {
60
52
  ...track.trackMenuItems(),
61
53
  ].sort((a, b) => ((b === null || b === void 0 ? void 0 : b.priority) || 0) - ((a === null || a === void 0 ? void 0 : a.priority) || 0));
62
54
  return (React.createElement(Paper, { ref: ref, className: cx(className, classes.root) },
63
- React.createElement("span", { draggable: true, className: classes.dragHandle, onDragStart: event => {
64
- const target = event.currentTarget;
65
- if (target.parentNode) {
66
- const parent = target.parentNode;
67
- event.dataTransfer.setDragImage(parent, 20, 20);
68
- view.setDraggingTrackId(track.id);
69
- }
70
- }, onDragEnd: () => view.setDraggingTrackId(undefined), "data-testid": `dragHandle-${view.id}-${trackId}` },
71
- React.createElement(DragIcon, { className: classes.dragHandleIcon, fontSize: "small" })),
55
+ React.createElement(TrackLabelDragHandle, { track: track, trackId: trackId, view: view }),
72
56
  React.createElement(IconButton, { onClick: () => view.hideTrack(trackId), className: classes.iconButton, title: "close this track" },
73
57
  React.createElement(CloseIcon, { fontSize: "small" })),
74
58
  React.createElement(Typography, { variant: "body1", component: "span", className: classes.trackName },
@@ -77,5 +61,5 @@ const TrackLabel = React.forwardRef(function ({ track, className }, ref) {
77
61
  .join(' ') })),
78
62
  React.createElement(CascadingMenuButton, { menuItems: items, "data-testid": "track_menu_icon" },
79
63
  React.createElement(MoreVertIcon, { fontSize: "small" }))));
80
- });
81
- export default observer(TrackLabel);
64
+ }));
65
+ export default TrackLabel;
@@ -0,0 +1,9 @@
1
+ import React from 'react';
2
+ import { BaseTrackModel } from '@jbrowse/core/pluggableElementTypes/models';
3
+ import { LinearGenomeViewModel } from '..';
4
+ declare function TrackLabelDragHandle({ trackId, view, track, }: {
5
+ trackId: string;
6
+ track: BaseTrackModel;
7
+ view: LinearGenomeViewModel;
8
+ }): React.JSX.Element;
9
+ export default TrackLabelDragHandle;
@@ -0,0 +1,27 @@
1
+ import React from 'react';
2
+ import { makeStyles } from 'tss-react/mui';
3
+ // icons
4
+ import DragIcon from '@mui/icons-material/DragIndicator';
5
+ const useStyles = makeStyles()({
6
+ dragHandle: {
7
+ cursor: 'grab',
8
+ },
9
+ dragHandleIcon: {
10
+ display: 'inline-block',
11
+ verticalAlign: 'middle',
12
+ pointerEvents: 'none',
13
+ },
14
+ });
15
+ function TrackLabelDragHandle({ trackId, view, track, }) {
16
+ const { classes } = useStyles();
17
+ return (React.createElement("span", { draggable: true, className: classes.dragHandle, onDragStart: event => {
18
+ const target = event.currentTarget;
19
+ if (target.parentNode) {
20
+ const parent = target.parentNode;
21
+ event.dataTransfer.setDragImage(parent, 20, 20);
22
+ view.setDraggingTrackId(track.id);
23
+ }
24
+ }, onDragEnd: () => view.setDraggingTrackId(undefined), "data-testid": `dragHandle-${view.id}-${trackId}` },
25
+ React.createElement(DragIcon, { className: classes.dragHandleIcon, fontSize: "small" })));
26
+ }
27
+ export default TrackLabelDragHandle;
@@ -2,9 +2,9 @@ import React from 'react';
2
2
  import { BaseTrackModel } from '@jbrowse/core/pluggableElementTypes/models';
3
3
  import { LinearGenomeViewModel } from '..';
4
4
  type LGV = LinearGenomeViewModel;
5
- declare const _default: ({ model, track, onDragEnter, }: {
5
+ declare const TrackRenderingContainer: ({ model, track, onDragEnter, }: {
6
6
  model: LGV;
7
7
  track: BaseTrackModel;
8
8
  onDragEnter: () => void;
9
9
  }) => React.JSX.Element;
10
- export default _default;
10
+ export default TrackRenderingContainer;
@@ -22,7 +22,7 @@ const useStyles = makeStyles()({
22
22
  zIndex: 2,
23
23
  },
24
24
  });
25
- export default observer(function TrackRenderingContainer({ model, track, onDragEnter, }) {
25
+ const TrackRenderingContainer = observer(function ({ model, track, onDragEnter, }) {
26
26
  const { classes } = useStyles();
27
27
  const display = track.displays[0];
28
28
  const { height, RenderingComponent, DisplayBlurb } = display;
@@ -48,3 +48,4 @@ export default observer(function TrackRenderingContainer({ model, track, onDragE
48
48
  } },
49
49
  React.createElement(DisplayBlurb, { model: display }))) : null)) : null));
50
50
  });
51
+ export default TrackRenderingContainer;
@@ -1,8 +1,8 @@
1
1
  import React from 'react';
2
2
  import { LinearGenomeViewModel } from '..';
3
3
  type LGV = LinearGenomeViewModel;
4
- declare const _default: ({ children, model, }: {
4
+ declare const TracksContainer: ({ children, model, }: {
5
5
  children: React.ReactNode;
6
6
  model: LGV;
7
7
  }) => React.JSX.Element;
8
- export default _default;
8
+ export default TracksContainer;
@@ -19,7 +19,7 @@ const useStyles = makeStyles()({
19
19
  overflow: 'hidden',
20
20
  },
21
21
  });
22
- export default observer(function TracksContainer({ children, model, }) {
22
+ const TracksContainer = observer(function TracksContainer({ children, model, }) {
23
23
  const { classes } = useStyles();
24
24
  const { pluginManager } = getEnv(model);
25
25
  const { mouseDown: mouseDown1, mouseUp } = useSideScroll(model);
@@ -42,3 +42,4 @@ export default observer(function TracksContainer({ children, model, }) {
42
42
  additional,
43
43
  children));
44
44
  });
45
+ export default TracksContainer;
@@ -1,9 +1,8 @@
1
1
  import React from 'react';
2
2
  import { LinearGenomeViewModel } from '..';
3
3
  type LGV = LinearGenomeViewModel;
4
- declare function VerticalGuide({ model, coordX }: {
4
+ declare const VerticalGuide: ({ model, coordX, }: {
5
5
  model: LGV;
6
6
  coordX: number;
7
- }): React.JSX.Element;
8
- declare const _default: typeof VerticalGuide;
9
- export default _default;
7
+ }) => React.JSX.Element;
8
+ export default VerticalGuide;
@@ -12,12 +12,12 @@ const useStyles = makeStyles()({
12
12
  zIndex: 10,
13
13
  },
14
14
  });
15
- function VerticalGuide({ model, coordX }) {
15
+ const VerticalGuide = observer(function VerticalGuide({ model, coordX, }) {
16
16
  const { classes } = useStyles();
17
17
  return (React.createElement(Tooltip, { open: true, placement: "top", title: stringify(model.pxToBp(coordX)), arrow: true },
18
18
  React.createElement("div", { className: classes.guide, style: {
19
19
  left: coordX,
20
20
  background: 'red',
21
21
  } })));
22
- }
23
- export default observer(VerticalGuide);
22
+ });
23
+ export default VerticalGuide;
@@ -1,7 +1,6 @@
1
1
  import React from 'react';
2
2
  import { LinearGenomeViewModel } from '..';
3
- declare function ZoomControls({ model }: {
3
+ declare const ZoomControls: ({ model, }: {
4
4
  model: LinearGenomeViewModel;
5
- }): React.JSX.Element;
6
- declare const _default: typeof ZoomControls;
7
- export default _default;
5
+ }) => React.JSX.Element;
6
+ export default ZoomControls;
@@ -15,7 +15,7 @@ const useStyles = makeStyles()(theme => ({
15
15
  color: theme.palette.text.secondary,
16
16
  },
17
17
  }));
18
- function ZoomControls({ model }) {
18
+ const ZoomControls = observer(function ({ model, }) {
19
19
  const { classes } = useStyles();
20
20
  const { maxBpPerPx, minBpPerPx, bpPerPx, scaleFactor } = model;
21
21
  const [value, setValue] = useState(-Math.log2(bpPerPx) * 100);
@@ -28,5 +28,5 @@ function ZoomControls({ model }) {
28
28
  React.createElement(Slider, { size: "small", className: classes.slider, value: value, min: -Math.log2(maxBpPerPx) * 100, max: -Math.log2(minBpPerPx) * 100, onChange: (_, val) => setValue(val), onChangeCommitted: () => model.zoomTo(2 ** (-value / 100)), disabled: scaleFactor !== 1 }),
29
29
  React.createElement(IconButton, { "data-testid": "zoom_in", onClick: () => model.zoom(model.bpPerPx / 2), disabled: bpPerPx <= minBpPerPx + 0.0001 || scaleFactor !== 1, size: "large" },
30
30
  React.createElement(ZoomIn, null))));
31
- }
32
- export default observer(ZoomControls);
31
+ });
32
+ export default ZoomControls;
@@ -20,5 +20,5 @@ export declare function getCytobands(assembly: Assembly | undefined, refName: st
20
20
  refName: string;
21
21
  start: number;
22
22
  end: number;
23
- type: any;
23
+ type: string;
24
24
  }[];
@@ -1,4 +1,3 @@
1
1
  import PluginManager from '@jbrowse/core/PluginManager';
2
- declare const _default: (pluginManager: PluginManager) => void;
3
- export default _default;
2
+ export default function LinearGenomeViewF(pluginManager: PluginManager): void;
4
3
  export * from './model';
@@ -1,7 +1,7 @@
1
1
  import { lazy } from 'react';
2
2
  import { ViewType } from '@jbrowse/core/pluggableElementTypes';
3
3
  import { stateModelFactory } from './model';
4
- export default (pluginManager) => {
4
+ export default function LinearGenomeViewF(pluginManager) {
5
5
  pluginManager.addViewType(() => {
6
6
  return new ViewType({
7
7
  name: 'LinearGenomeView',
@@ -10,5 +10,5 @@ export default (pluginManager) => {
10
10
  ReactComponent: lazy(() => import('./components/LinearGenomeView')),
11
11
  });
12
12
  });
13
- };
13
+ }
14
14
  export * from './model';
@@ -87,12 +87,10 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
87
87
  volatileWidth: number | undefined;
88
88
  minimumBlockWidth: number;
89
89
  draggingTrackId: string | undefined;
90
- volatileError: Error | undefined;
90
+ volatileError: unknown;
91
91
  afterDisplayedRegionsSetCallbacks: Function[];
92
92
  scaleFactor: number;
93
- trackRefs: {
94
- [key: string]: HTMLDivElement;
95
- };
93
+ trackRefs: Record<string, HTMLDivElement>;
96
94
  coarseDynamicBlocks: BaseBlock[];
97
95
  coarseTotalBp: number;
98
96
  leftOffset: BpOffset | undefined;
@@ -170,7 +168,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
170
168
  /**
171
169
  * #getter
172
170
  */
173
- readonly error: string | Error;
171
+ readonly error: {};
174
172
  /**
175
173
  * #getter
176
174
  */
@@ -224,7 +222,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
224
222
  /**
225
223
  * #action
226
224
  */
227
- setError(error: Error | undefined): void;
225
+ setError(error: unknown): void;
228
226
  /**
229
227
  * #action
230
228
  */
@@ -545,6 +543,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
545
543
  end: number;
546
544
  reversed: boolean;
547
545
  } | undefined;
546
+ } & {
547
+ afterCreate(): void;
548
548
  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
549
549
  export type LinearGenomeViewStateModel = ReturnType<typeof stateModelFactory>;
550
550
  export type LinearGenomeViewModel = Instance<LinearGenomeViewStateModel>;
@@ -1227,6 +1227,39 @@ export function stateModelFactory(pluginManager) {
1227
1227
  ? this.pxToBp(self.width / 2)
1228
1228
  : undefined;
1229
1229
  },
1230
+ }))
1231
+ .actions(self => ({
1232
+ afterCreate() {
1233
+ function handler(e) {
1234
+ const session = getSession(self);
1235
+ if (session.focusedViewId === self.id && (e.ctrlKey || e.metaKey)) {
1236
+ if (e.code === 'ArrowLeft') {
1237
+ e.preventDefault();
1238
+ // pan left
1239
+ self.slide(-0.9);
1240
+ }
1241
+ if (e.code === 'ArrowRight') {
1242
+ e.preventDefault();
1243
+ // pan right
1244
+ self.slide(0.9);
1245
+ }
1246
+ if (e.code === 'ArrowUp' && self.scaleFactor === 1) {
1247
+ e.preventDefault();
1248
+ // zoom in
1249
+ self.zoom(self.bpPerPx / 2);
1250
+ }
1251
+ if (e.code === 'ArrowDown' && self.scaleFactor === 1) {
1252
+ e.preventDefault();
1253
+ // zoom out
1254
+ self.zoom(self.bpPerPx * 2);
1255
+ }
1256
+ }
1257
+ }
1258
+ document.addEventListener('keydown', handler);
1259
+ addDisposer(self, () => {
1260
+ document.removeEventListener('keydown', handler);
1261
+ });
1262
+ },
1230
1263
  }));
1231
1264
  }
1232
1265
  export { default as ReactComponent, default as LinearGenomeView, } from './components/LinearGenomeView';
@@ -1,7 +1,7 @@
1
1
  import React from 'react';
2
2
  import { useTheme } from '@mui/material';
3
- import Color from 'color';
3
+ import { stripAlpha } from '@jbrowse/core/util';
4
4
  export default function SVGBackground({ width, height, shift, }) {
5
5
  const theme = useTheme();
6
- return (React.createElement("rect", { width: width + shift * 2, height: height, fill: Color(theme.palette.background.default).hex() }));
6
+ return (React.createElement("rect", { width: width + shift * 2, height: height, fill: stripAlpha(theme.palette.background.default) }));
7
7
  }
@@ -1,8 +1,7 @@
1
1
  import React from 'react';
2
- import { getSession } from '@jbrowse/core/util';
2
+ import { getSession, stripAlpha } from '@jbrowse/core/util';
3
3
  import Base1DView from '@jbrowse/core/util/Base1DViewModel';
4
4
  import { useTheme } from '@mui/material';
5
- import Color from 'color';
6
5
  // locals
7
6
  import { HEADER_OVERVIEW_HEIGHT } from '..';
8
7
  import Cytobands from '../components/Cytobands';
@@ -15,7 +14,7 @@ export default function SVGHeader({ model, fontSize, cytobandHeight, rulerHeight
15
14
  const assemblyName = assemblyNames.length > 1 ? '' : assemblyNames[0];
16
15
  const assembly = assemblyManager.get(assemblyName);
17
16
  const theme = useTheme();
18
- const c = Color(theme.palette.text.primary).hex();
17
+ const c = stripAlpha(theme.palette.text.primary);
19
18
  const overview = Base1DView.create({
20
19
  displayedRegions: JSON.parse(JSON.stringify(displayedRegions)),
21
20
  interRegionPaddingWidth: 0,
@@ -28,9 +27,7 @@ export default function SVGHeader({ model, fontSize, cytobandHeight, rulerHeight
28
27
  overview.setVolatileWidth(width);
29
28
  overview.showAllRegions();
30
29
  const block = overview.dynamicBlocks.contentBlocks[0];
31
- // eslint-disable-next-line @typescript-eslint/no-non-null-assertion
32
30
  const first = visibleRegions.at(0);
33
- // eslint-disable-next-line @typescript-eslint/no-non-null-assertion
34
31
  const last = visibleRegions.at(-1);
35
32
  const firstOverviewPx = overview.bpToPx({
36
33
  ...first,
@@ -1,3 +1,4 @@
1
+ /* eslint-disable react-refresh/only-export-components */
1
2
  import React from 'react';
2
3
  import { renderToStaticMarkup } from 'react-dom/server';
3
4
  import { when } from 'mobx';
@@ -1,14 +1,13 @@
1
1
  import React from 'react';
2
- import { getTickDisplayStr } from '@jbrowse/core/util';
2
+ import { getTickDisplayStr, stripAlpha } from '@jbrowse/core/util';
3
3
  import { useTheme } from '@mui/material';
4
4
  // locals
5
5
  import { makeTicks } from '../util';
6
6
  import SVGRegionSeparators from './SVGRegionSeparators';
7
- import Color from 'color';
8
7
  function Ruler({ start, end, bpPerPx, reversed = false, major = true, minor = true, hideText = false, }) {
9
8
  const ticks = makeTicks(start, end, bpPerPx, major, minor);
10
9
  const theme = useTheme();
11
- const c = Color(theme.palette.text.secondary).hex();
10
+ const c = stripAlpha(theme.palette.text.secondary);
12
11
  return (React.createElement(React.Fragment, null,
13
12
  ticks.map(tick => {
14
13
  const x = (reversed ? end - tick.base : tick.base - start) / bpPerPx;
@@ -27,7 +26,7 @@ export default function SVGRuler({ model, fontSize, }) {
27
26
  const { dynamicBlocks: { contentBlocks }, offsetPx: viewOffsetPx, bpPerPx, } = model;
28
27
  const renderRuler = contentBlocks.length < 5;
29
28
  const theme = useTheme();
30
- const c = Color(theme.palette.text.primary).hex();
29
+ const c = stripAlpha(theme.palette.text.primary);
31
30
  return (React.createElement(React.Fragment, null,
32
31
  React.createElement(SVGRegionSeparators, { model: model, height: 30 }),
33
32
  contentBlocks.map(block => {
@@ -1,14 +1,13 @@
1
1
  import React from 'react';
2
- import { getBpDisplayStr } from '@jbrowse/core/util';
2
+ import { getBpDisplayStr, stripAlpha } from '@jbrowse/core/util';
3
3
  import { useTheme } from '@mui/material';
4
- import Color from 'color';
5
4
  export default function SVGScalebar({ model, fontSize, }) {
6
5
  const { offsetPx, dynamicBlocks: { totalWidthPxWithoutBorders: totalWidthPx, totalBp }, } = model;
7
6
  const theme = useTheme();
8
7
  const displayBp = getBpDisplayStr(totalBp);
9
8
  const x0 = Math.max(-offsetPx, 0);
10
9
  const x1 = x0 + totalWidthPx;
11
- const c = Color(theme.palette.text.secondary).hex();
10
+ const c = stripAlpha(theme.palette.text.secondary);
12
11
  const x = x0 + (x1 - x0) / 2;
13
12
  const y = fontSize;
14
13
  return (React.createElement(React.Fragment, null,
@@ -1,9 +1,11 @@
1
1
  import React from 'react';
2
2
  import { useTheme } from '@mui/material';
3
+ import { coarseStripHTML } from '@jbrowse/core/util';
3
4
  export default function SVGTrackLabel({ trackLabels, trackName, fontSize, trackLabelOffset, x, }) {
4
5
  const theme = useTheme();
5
6
  const fill = theme.palette.text.primary;
6
7
  const xoff = trackLabels === 'overlay' ? 5 : 0;
7
8
  const yoff = trackLabels === 'offset' ? 5 : 0;
8
- return trackLabels !== 'none' ? (React.createElement("g", null, trackLabels === 'left' ? (React.createElement("text", { x: trackLabelOffset - 40, y: 20, fill: fill, fontSize: fontSize, dominantBaseline: "hanging", textAnchor: "end" }, trackName)) : (React.createElement("text", { x: x + xoff, y: yoff, fill: fill, fontSize: fontSize, dominantBaseline: "hanging" }, trackName)))) : null;
9
+ const name = coarseStripHTML(trackName);
10
+ return trackLabels !== 'none' ? (React.createElement("g", null, trackLabels === 'left' ? (React.createElement("text", { x: trackLabelOffset - 40, y: 20, fill: fill, fontSize: fontSize, dominantBaseline: "hanging", textAnchor: "end" }, name)) : (React.createElement("text", { x: x + xoff, y: yoff, fill: fill, fontSize: fontSize, dominantBaseline: "hanging" }, name)))) : null;
9
11
  }