@jbrowse/plugin-wiggle 1.7.10 → 2.0.1

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 (140) hide show
  1. package/dist/BigWigAdapter/BigWigAdapter.js +176 -284
  2. package/dist/BigWigAdapter/BigWigAdapter.js.map +1 -0
  3. package/dist/BigWigAdapter/configSchema.js +12 -21
  4. package/dist/BigWigAdapter/configSchema.js.map +1 -0
  5. package/dist/BigWigAdapter/index.js +8 -14
  6. package/dist/BigWigAdapter/index.js.map +1 -0
  7. package/dist/DensityRenderer/index.d.ts +1 -1
  8. package/dist/DensityRenderer/index.js +152 -133
  9. package/dist/DensityRenderer/index.js.map +1 -0
  10. package/dist/LinePlotRenderer/LinePlotRenderer.d.ts +1 -1
  11. package/dist/LinePlotRenderer/LinePlotRenderer.js +182 -168
  12. package/dist/LinePlotRenderer/LinePlotRenderer.js.map +1 -0
  13. package/dist/LinePlotRenderer/index.js +19 -33
  14. package/dist/LinePlotRenderer/index.js.map +1 -0
  15. package/dist/LinearWiggleDisplay/components/SetColorDialog.js +95 -105
  16. package/dist/LinearWiggleDisplay/components/SetColorDialog.js.map +1 -0
  17. package/dist/LinearWiggleDisplay/components/SetMinMaxDialog.js +86 -107
  18. package/dist/LinearWiggleDisplay/components/SetMinMaxDialog.js.map +1 -0
  19. package/dist/LinearWiggleDisplay/components/Tooltip.js +147 -152
  20. package/dist/LinearWiggleDisplay/components/Tooltip.js.map +1 -0
  21. package/dist/LinearWiggleDisplay/components/WiggleDisplayComponent.js +44 -50
  22. package/dist/LinearWiggleDisplay/components/WiggleDisplayComponent.js.map +1 -0
  23. package/dist/LinearWiggleDisplay/components/YScaleBar.js +24 -31
  24. package/dist/LinearWiggleDisplay/components/YScaleBar.js.map +1 -0
  25. package/dist/LinearWiggleDisplay/index.js +13 -42
  26. package/dist/LinearWiggleDisplay/index.js.map +1 -0
  27. package/dist/LinearWiggleDisplay/models/configSchema.js +65 -69
  28. package/dist/LinearWiggleDisplay/models/configSchema.js.map +1 -0
  29. package/dist/LinearWiggleDisplay/models/model.d.ts +16 -14
  30. package/dist/LinearWiggleDisplay/models/model.js +585 -696
  31. package/dist/LinearWiggleDisplay/models/model.js.map +1 -0
  32. package/dist/WiggleBaseRenderer.d.ts +3 -3
  33. package/dist/WiggleBaseRenderer.js +119 -129
  34. package/dist/WiggleBaseRenderer.js.map +1 -0
  35. package/dist/WiggleRPC/rpcMethods.js +182 -288
  36. package/dist/WiggleRPC/rpcMethods.js.map +1 -0
  37. package/dist/WiggleRendering.js +107 -102
  38. package/dist/WiggleRendering.js.map +1 -0
  39. package/dist/XYPlotRenderer/XYPlotRenderer.d.ts +1 -1
  40. package/dist/XYPlotRenderer/XYPlotRenderer.js +250 -194
  41. package/dist/XYPlotRenderer/XYPlotRenderer.js.map +1 -0
  42. package/dist/XYPlotRenderer/index.js +30 -33
  43. package/dist/XYPlotRenderer/index.js.map +1 -0
  44. package/dist/configSchema.js +47 -74
  45. package/dist/configSchema.js.map +1 -0
  46. package/dist/index.d.ts +118 -67
  47. package/dist/index.js +167 -242
  48. package/dist/index.js.map +1 -0
  49. package/dist/util.js +112 -143
  50. package/dist/util.js.map +1 -0
  51. package/esm/BigWigAdapter/BigWigAdapter.d.ts +24 -0
  52. package/esm/BigWigAdapter/BigWigAdapter.js +62 -0
  53. package/esm/BigWigAdapter/BigWigAdapter.js.map +1 -0
  54. package/{dist/LinePlotRenderer → esm/BigWigAdapter}/configSchema.d.ts +0 -0
  55. package/esm/BigWigAdapter/configSchema.js +11 -0
  56. package/esm/BigWigAdapter/configSchema.js.map +1 -0
  57. package/esm/BigWigAdapter/index.d.ts +1 -0
  58. package/esm/BigWigAdapter/index.js +2 -0
  59. package/esm/BigWigAdapter/index.js.map +1 -0
  60. package/esm/DensityRenderer/index.d.ts +6 -0
  61. package/esm/DensityRenderer/index.js +39 -0
  62. package/esm/DensityRenderer/index.js.map +1 -0
  63. package/esm/LinePlotRenderer/LinePlotRenderer.d.ts +4 -0
  64. package/esm/LinePlotRenderer/LinePlotRenderer.js +71 -0
  65. package/esm/LinePlotRenderer/LinePlotRenderer.js.map +1 -0
  66. package/esm/LinePlotRenderer/index.d.ts +3 -0
  67. package/esm/LinePlotRenderer/index.js +12 -0
  68. package/esm/LinePlotRenderer/index.js.map +1 -0
  69. package/esm/LinearWiggleDisplay/components/SetColorDialog.d.ts +10 -0
  70. package/esm/LinearWiggleDisplay/components/SetColorDialog.js +55 -0
  71. package/esm/LinearWiggleDisplay/components/SetColorDialog.js.map +1 -0
  72. package/esm/LinearWiggleDisplay/components/SetMinMaxDialog.d.ts +11 -0
  73. package/esm/LinearWiggleDisplay/components/SetMinMaxDialog.js +46 -0
  74. package/esm/LinearWiggleDisplay/components/SetMinMaxDialog.js.map +1 -0
  75. package/esm/LinearWiggleDisplay/components/Tooltip.d.ts +24 -0
  76. package/esm/LinearWiggleDisplay/components/Tooltip.js +107 -0
  77. package/esm/LinearWiggleDisplay/components/Tooltip.js.map +1 -0
  78. package/esm/LinearWiggleDisplay/components/WiggleDisplayComponent.d.ts +8 -0
  79. package/esm/LinearWiggleDisplay/components/WiggleDisplayComponent.js +29 -0
  80. package/esm/LinearWiggleDisplay/components/WiggleDisplayComponent.js.map +1 -0
  81. package/esm/LinearWiggleDisplay/components/YScaleBar.d.ts +7 -0
  82. package/esm/LinearWiggleDisplay/components/YScaleBar.js +9 -0
  83. package/esm/LinearWiggleDisplay/components/YScaleBar.js.map +1 -0
  84. package/esm/LinearWiggleDisplay/index.d.ts +3 -0
  85. package/esm/LinearWiggleDisplay/index.js +4 -0
  86. package/esm/LinearWiggleDisplay/index.js.map +1 -0
  87. package/esm/LinearWiggleDisplay/models/configSchema.d.ts +2 -0
  88. package/esm/LinearWiggleDisplay/models/configSchema.js +64 -0
  89. package/esm/LinearWiggleDisplay/models/configSchema.js.map +1 -0
  90. package/esm/LinearWiggleDisplay/models/model.d.ts +290 -0
  91. package/esm/LinearWiggleDisplay/models/model.js +495 -0
  92. package/esm/LinearWiggleDisplay/models/model.js.map +1 -0
  93. package/esm/WiggleBaseRenderer.d.ts +55 -0
  94. package/esm/WiggleBaseRenderer.js +34 -0
  95. package/esm/WiggleBaseRenderer.js.map +1 -0
  96. package/esm/WiggleRPC/rpcMethods.d.ts +31 -0
  97. package/esm/WiggleRPC/rpcMethods.js +70 -0
  98. package/esm/WiggleRPC/rpcMethods.js.map +1 -0
  99. package/esm/WiggleRendering.d.ts +16 -0
  100. package/esm/WiggleRendering.js +40 -0
  101. package/esm/WiggleRendering.js.map +1 -0
  102. package/esm/XYPlotRenderer/XYPlotRenderer.d.ts +4 -0
  103. package/esm/XYPlotRenderer/XYPlotRenderer.js +109 -0
  104. package/esm/XYPlotRenderer/XYPlotRenderer.js.map +1 -0
  105. package/esm/XYPlotRenderer/index.d.ts +3 -0
  106. package/esm/XYPlotRenderer/index.js +23 -0
  107. package/esm/XYPlotRenderer/index.js.map +1 -0
  108. package/esm/configSchema.d.ts +2 -0
  109. package/esm/configSchema.js +46 -0
  110. package/esm/configSchema.js.map +1 -0
  111. package/esm/index.d.ts +917 -0
  112. package/esm/index.js +115 -0
  113. package/esm/index.js.map +1 -0
  114. package/esm/util.d.ts +41 -0
  115. package/esm/util.js +123 -0
  116. package/esm/util.js.map +1 -0
  117. package/package.json +23 -15
  118. package/src/DensityRenderer/DensityRenderer.test.js +5 -0
  119. package/src/DensityRenderer/index.ts +1 -1
  120. package/src/LinePlotRenderer/LinePlotRenderer.js +1 -1
  121. package/src/LinePlotRenderer/index.js +7 -1
  122. package/src/LinearWiggleDisplay/components/SetColorDialog.tsx +10 -13
  123. package/src/LinearWiggleDisplay/components/SetMinMaxDialog.tsx +13 -11
  124. package/src/LinearWiggleDisplay/components/Tooltip.tsx +4 -3
  125. package/src/LinearWiggleDisplay/components/WiggleDisplayComponent.tsx +9 -4
  126. package/src/LinearWiggleDisplay/models/model.tsx +56 -65
  127. package/src/WiggleBaseRenderer.tsx +3 -3
  128. package/src/XYPlotRenderer/XYPlotRenderer.test.js +5 -0
  129. package/src/XYPlotRenderer/XYPlotRenderer.ts +87 -40
  130. package/src/XYPlotRenderer/index.ts +19 -2
  131. package/src/configSchema.ts +0 -23
  132. package/dist/BigWigAdapter/BigWigAdapter.test.js +0 -157
  133. package/dist/DensityRenderer/DensityRenderer.test.js +0 -84
  134. package/dist/LinePlotRenderer/configSchema.js +0 -70
  135. package/dist/WiggleRendering.test.js +0 -52
  136. package/dist/XYPlotRenderer/XYPlotRenderer.test.js +0 -83
  137. package/dist/declare.d.js +0 -1
  138. package/dist/index.test.js +0 -24
  139. package/dist/util.test.js +0 -66
  140. package/src/LinePlotRenderer/configSchema.js +0 -68
@@ -0,0 +1,55 @@
1
+ import React, { useState } from 'react';
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+ import { Button, Dialog, DialogContent, DialogActions, DialogTitle, FormControlLabel, IconButton, Radio, Typography, } from '@mui/material';
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+ import { makeStyles } from 'tss-react/mui';
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+ import CloseIcon from '@mui/icons-material/Close';
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+ import { CompactPicker } from 'react-color';
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+ const useStyles = makeStyles()(theme => ({
7
+ closeButton: {
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+ position: 'absolute',
9
+ right: theme.spacing(1),
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+ top: theme.spacing(1),
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+ color: theme.palette.grey[500],
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+ },
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+ }));
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+ // this is needed because passing a entire color object into the react-color
15
+ // for alpha, can't pass in an rgba string for example
16
+ function serialize(color) {
17
+ if (color instanceof Object) {
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+ const { r, g, b } = color;
19
+ return `rgb(${r},${g},${b})`;
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+ }
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+ return color;
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+ }
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+ export default function SetColorDialog({ model, handleClose, }) {
24
+ const { classes } = useStyles();
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+ const [posneg, setPosNeg] = useState(false);
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+ return (React.createElement(Dialog, { open: true, onClose: handleClose },
27
+ React.createElement(DialogTitle, null,
28
+ "Select either an overall color, or the positive/negative colors. Note that density renderers only work properly with positive/negative colors",
29
+ React.createElement(IconButton, { "aria-label": "close", className: classes.closeButton, onClick: handleClose },
30
+ React.createElement(CloseIcon, null))),
31
+ React.createElement(DialogContent, null,
32
+ React.createElement(FormControlLabel, { checked: !posneg, onClick: () => setPosNeg(false), control: React.createElement(Radio, null), label: 'Overall color' }),
33
+ React.createElement(FormControlLabel, { checked: posneg, onClick: () => setPosNeg(true), control: React.createElement(Radio, null), label: 'Positive/negative color' }),
34
+ posneg ? (React.createElement(React.Fragment, null,
35
+ React.createElement(Typography, null, "Positive color"),
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+ React.createElement(CompactPicker, { onChange: event => {
37
+ model.setPosColor(serialize(event.rgb));
38
+ model.setColor(undefined);
39
+ } }),
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+ React.createElement(Typography, null, "Negative color"),
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+ React.createElement(CompactPicker, { onChange: event => {
42
+ model.setNegColor(serialize(event.rgb));
43
+ model.setColor(undefined);
44
+ } }))) : (React.createElement(React.Fragment, null,
45
+ React.createElement(Typography, null, "Overall color"),
46
+ React.createElement(CompactPicker, { onChange: event => model.setColor(serialize(event.rgb)) })))),
47
+ React.createElement(DialogActions, null,
48
+ React.createElement(Button, { onClick: () => {
49
+ model.setPosColor(undefined);
50
+ model.setNegColor(undefined);
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+ model.setColor(undefined);
52
+ }, color: "secondary", variant: "contained" }, "Restore default"),
53
+ React.createElement(Button, { variant: "contained", color: "primary", type: "submit", onClick: () => handleClose() }, "Submit"))));
54
+ }
55
+ //# sourceMappingURL=SetColorDialog.js.map
@@ -0,0 +1 @@
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@@ -0,0 +1,11 @@
1
+ /// <reference types="react" />
2
+ export default function SetMinMaxDlg(props: {
3
+ model: {
4
+ minScore: number;
5
+ maxScore: number;
6
+ scaleType: string;
7
+ setMinScore: Function;
8
+ setMaxScore: Function;
9
+ };
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+ handleClose: () => void;
11
+ }): JSX.Element;
@@ -0,0 +1,46 @@
1
+ import React, { useState } from 'react';
2
+ import { Button, Dialog, DialogContent, DialogTitle, IconButton, TextField, Typography, } from '@mui/material';
3
+ import { makeStyles } from 'tss-react/mui';
4
+ import CloseIcon from '@mui/icons-material/Close';
5
+ const useStyles = makeStyles()(theme => ({
6
+ root: {},
7
+ closeButton: {
8
+ position: 'absolute',
9
+ right: theme.spacing(1),
10
+ top: theme.spacing(1),
11
+ color: theme.palette.grey[500],
12
+ },
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+ }));
14
+ export default function SetMinMaxDlg(props) {
15
+ const { classes } = useStyles();
16
+ const { model, handleClose } = props;
17
+ const { minScore, maxScore, scaleType } = model;
18
+ const [min, setMin] = useState(`${minScore !== Number.MIN_VALUE ? minScore : ''}`);
19
+ const [max, setMax] = useState(`${maxScore !== Number.MAX_VALUE ? maxScore : ''}`);
20
+ const ok = min !== '' && max !== '' && !Number.isNaN(+min) && !Number.isNaN(+max)
21
+ ? +max > +min
22
+ : true;
23
+ const logOk = scaleType === 'log' && min !== '' && !Number.isNaN(+min) ? +min > 0 : true;
24
+ return (React.createElement(Dialog, { open: true, onClose: handleClose },
25
+ React.createElement(DialogTitle, null,
26
+ "Set min/max score for track",
27
+ React.createElement(IconButton, { className: classes.closeButton, onClick: handleClose },
28
+ React.createElement(CloseIcon, null))),
29
+ React.createElement(DialogContent, { style: { overflowX: 'hidden' } },
30
+ React.createElement("div", { className: classes.root },
31
+ React.createElement(Typography, null, "Enter min/max score: "),
32
+ !ok ? (React.createElement(Typography, { color: "error" }, "Max is greater than or equal to min")) : null,
33
+ !logOk ? (React.createElement(Typography, { color: "error" }, "Min score should be greater than 0 for log scale")) : null,
34
+ React.createElement(TextField, { value: min, onChange: event => {
35
+ setMin(event.target.value);
36
+ }, placeholder: "Enter min score" }),
37
+ React.createElement(TextField, { value: max, onChange: event => {
38
+ setMax(event.target.value);
39
+ }, placeholder: "Enter max score" }),
40
+ React.createElement(Button, { variant: "contained", color: "primary", type: "submit", style: { marginLeft: 20 }, disabled: !ok, onClick: () => {
41
+ model.setMinScore(min !== '' && !Number.isNaN(+min) ? +min : undefined);
42
+ model.setMaxScore(max !== '' && !Number.isNaN(+max) ? +max : undefined);
43
+ handleClose();
44
+ } }, "Submit")))));
45
+ }
46
+ //# sourceMappingURL=SetMinMaxDialog.js.map
@@ -0,0 +1 @@
1
+ {"version":3,"file":"SetMinMaxDialog.js","sourceRoot":"","sources":["../../../src/LinearWiggleDisplay/components/SetMinMaxDialog.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AACvC,OAAO,EACL,MAAM,EACN,MAAM,EACN,aAAa,EACb,WAAW,EACX,UAAU,EACV,SAAS,EACT,UAAU,GACX,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,SAAS,MAAM,2BAA2B,CAAA;AAEjD,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,IAAI,EAAE,EAAE;IACR,WAAW,EAAE;QACX,QAAQ,EAAE,UAAU;QACpB,KAAK,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;QACvB,GAAG,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;QACrB,KAAK,EAAE,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC;KAC/B;CACF,CAAC,CAAC,CAAA;AAEH,MAAM,CAAC,OAAO,UAAU,YAAY,CAAC,KASpC;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,KAAK,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IACpC,MAAM,EAAE,QAAQ,EAAE,QAAQ,EAAE,SAAS,EAAE,GAAG,KAAK,CAAA;IAE/C,MAAM,CAAC,GAAG,EAAE,MAAM,CAAC,GAAG,QAAQ,CAC5B,GAAG,QAAQ,KAAK,MAAM,CAAC,SAAS,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,EAAE,EAAE,CACnD,CAAA;IACD,MAAM,CAAC,GAAG,EAAE,MAAM,CAAC,GAAG,QAAQ,CAC5B,GAAG,QAAQ,KAAK,MAAM,CAAC,SAAS,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,EAAE,EAAE,CACnD,CAAA;IAED,MAAM,EAAE,GACN,GAAG,KAAK,EAAE,IAAI,GAAG,KAAK,EAAE,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,GAAG,CAAC,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,GAAG,CAAC;QACpE,CAAC,CAAC,CAAC,GAAG,GAAG,CAAC,GAAG;QACb,CAAC,CAAC,IAAI,CAAA;IAEV,MAAM,KAAK,GACT,SAAS,KAAK,KAAK,IAAI,GAAG,KAAK,EAAE,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,GAAG,CAAC,CAAC,CAAC,CAAC,IAAI,CAAA;IAE5E,OAAO,CACL,oBAAC,MAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW;QAC/B,oBAAC,WAAW;;YAEV,oBAAC,UAAU,IAAC,SAAS,EAAE,OAAO,CAAC,WAAW,EAAE,OAAO,EAAE,WAAW;gBAC9D,oBAAC,SAAS,OAAG,CACF,CACD;QACd,oBAAC,aAAa,IAAC,KAAK,EAAE,EAAE,SAAS,EAAE,QAAQ,EAAE;YAC3C,6BAAK,SAAS,EAAE,OAAO,CAAC,IAAI;gBAC1B,oBAAC,UAAU,gCAAmC;gBAC7C,CAAC,EAAE,CAAC,CAAC,CAAC,CACL,oBAAC,UAAU,IAAC,KAAK,EAAC,OAAO,0CAEZ,CACd,CAAC,CAAC,CAAC,IAAI;gBAEP,CAAC,KAAK,CAAC,CAAC,CAAC,CACR,oBAAC,UAAU,IAAC,KAAK,EAAC,OAAO,uDAEZ,CACd,CAAC,CAAC,CAAC,IAAI;gBAER,oBAAC,SAAS,IACR,KAAK,EAAE,GAAG,EACV,QAAQ,EAAE,KAAK,CAAC,EAAE;wBAChB,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;oBAC5B,CAAC,EACD,WAAW,EAAC,iBAAiB,GAC7B;gBACF,oBAAC,SAAS,IACR,KAAK,EAAE,GAAG,EACV,QAAQ,EAAE,KAAK,CAAC,EAAE;wBAChB,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;oBAC5B,CAAC,EACD,WAAW,EAAC,iBAAiB,GAC7B;gBAEF,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,IAAI,EAAC,QAAQ,EACb,KAAK,EAAE,EAAE,UAAU,EAAE,EAAE,EAAE,EACzB,QAAQ,EAAE,CAAC,EAAE,EACb,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,WAAW,CACf,GAAG,KAAK,EAAE,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,SAAS,CACrD,CAAA;wBACD,KAAK,CAAC,WAAW,CACf,GAAG,KAAK,EAAE,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,SAAS,CACrD,CAAA;wBACD,WAAW,EAAE,CAAA;oBACf,CAAC,aAGM,CACL,CACQ,CACT,CACV,CAAA;AACH,CAAC"}
@@ -0,0 +1,24 @@
1
+ import React from 'react';
2
+ import { Feature } from '@jbrowse/core/util/simpleFeature';
3
+ declare type Coord = [number, number];
4
+ declare const Tooltip: ({ model, height, clientMouseCoord, offsetMouseCoord, clientRect, TooltipContents, }: {
5
+ model: {
6
+ featureUnderMouse: Feature;
7
+ };
8
+ height: number;
9
+ clientMouseCoord: Coord;
10
+ offsetMouseCoord: Coord;
11
+ clientRect?: DOMRect | undefined;
12
+ TooltipContents: React.FC<any>;
13
+ }) => JSX.Element | null;
14
+ declare const WiggleTooltip: (props: {
15
+ model: {
16
+ featureUnderMouse: Feature;
17
+ };
18
+ height: number;
19
+ offsetMouseCoord: Coord;
20
+ clientMouseCoord: Coord;
21
+ clientRect?: DOMRect;
22
+ }) => JSX.Element;
23
+ export default WiggleTooltip;
24
+ export { Tooltip };
@@ -0,0 +1,107 @@
1
+ import React, { useMemo, useState } from 'react';
2
+ import { observer } from 'mobx-react';
3
+ import { alpha, Portal } from '@mui/material';
4
+ import { makeStyles } from 'tss-react/mui';
5
+ // locals
6
+ import { YSCALEBAR_LABEL_OFFSET } from '../models/model';
7
+ import { usePopper } from 'react-popper';
8
+ // convert to number, apply shortened precision, and render
9
+ function toP(s = 0) {
10
+ return +(+s).toPrecision(6);
11
+ }
12
+ function round(value) {
13
+ return Math.round(value * 1e5) / 1e5;
14
+ }
15
+ const en = (n) => n.toLocaleString('en-US');
16
+ const useStyles = makeStyles()(theme => ({
17
+ // these styles come from
18
+ // https://github.com/mui-org/material-ui/blob/master/packages/material-ui/src/Tooltip/Tooltip.js
19
+ tooltip: {
20
+ position: 'absolute',
21
+ pointerEvents: 'none',
22
+ backgroundColor: alpha(theme.palette.grey[700], 0.9),
23
+ borderRadius: theme.shape.borderRadius,
24
+ color: theme.palette.common.white,
25
+ fontFamily: theme.typography.fontFamily,
26
+ padding: '4px 8px',
27
+ fontSize: theme.typography.pxToRem(12),
28
+ lineHeight: `${round(14 / 10)}em`,
29
+ maxWidth: 300,
30
+ wordWrap: 'break-word',
31
+ },
32
+ hoverVertical: {
33
+ background: '#333',
34
+ border: 'none',
35
+ width: 1,
36
+ height: '100%',
37
+ top: YSCALEBAR_LABEL_OFFSET,
38
+ cursor: 'default',
39
+ position: 'absolute',
40
+ pointerEvents: 'none',
41
+ },
42
+ }));
43
+ const TooltipContents = React.forwardRef(({ feature }, ref) => {
44
+ const start = feature.get('start');
45
+ const end = feature.get('end');
46
+ const name = feature.get('refName');
47
+ const loc = [name, start === end ? en(start) : `${en(start)}..${en(end)}`]
48
+ .filter(f => !!f)
49
+ .join(':');
50
+ return feature.get('summary') !== undefined ? (React.createElement("div", { ref: ref },
51
+ loc,
52
+ React.createElement("br", null),
53
+ "Max: ",
54
+ toP(feature.get('maxScore')),
55
+ React.createElement("br", null),
56
+ "Avg: ",
57
+ toP(feature.get('score')),
58
+ React.createElement("br", null),
59
+ "Min: ",
60
+ toP(feature.get('minScore')))) : (React.createElement("div", { ref: ref },
61
+ loc,
62
+ React.createElement("br", null),
63
+ `${toP(feature.get('score'))}`));
64
+ });
65
+ const Tooltip = observer(({ model, height, clientMouseCoord, offsetMouseCoord, clientRect, TooltipContents, }) => {
66
+ const { featureUnderMouse } = model;
67
+ const [width, setWidth] = useState(0);
68
+ const [anchorEl, setAnchorEl] = useState(null);
69
+ const { classes } = useStyles();
70
+ // must be memoized a la https://github.com/popperjs/react-popper/issues/391
71
+ const virtElement = useMemo(() => ({
72
+ getBoundingClientRect: () => {
73
+ const x = clientMouseCoord[0] + width / 2 + 20;
74
+ const y = (clientRect === null || clientRect === void 0 ? void 0 : clientRect.top) || 0;
75
+ return {
76
+ top: y,
77
+ left: x,
78
+ bottom: y,
79
+ right: x,
80
+ width: 0,
81
+ height: 0,
82
+ x,
83
+ y,
84
+ toJSON() { },
85
+ };
86
+ },
87
+ }), [clientRect === null || clientRect === void 0 ? void 0 : clientRect.top, clientMouseCoord, width]);
88
+ const { styles, attributes } = usePopper(virtElement, anchorEl);
89
+ return featureUnderMouse ? (React.createElement(React.Fragment, null,
90
+ React.createElement(Portal, null,
91
+ React.createElement("div", { ref: setAnchorEl, className: classes.tooltip,
92
+ // zIndex needed to go over widget drawer
93
+ style: { ...styles.popper, zIndex: 100000 }, ...attributes.popper },
94
+ React.createElement(TooltipContents, { ref: (elt) => {
95
+ setWidth((elt === null || elt === void 0 ? void 0 : elt.getBoundingClientRect().width) || 0);
96
+ }, feature: featureUnderMouse }))),
97
+ React.createElement("div", { className: classes.hoverVertical, style: {
98
+ left: offsetMouseCoord[0],
99
+ height: height - YSCALEBAR_LABEL_OFFSET * 2,
100
+ } }))) : null;
101
+ });
102
+ const WiggleTooltip = observer((props) => {
103
+ return React.createElement(Tooltip, { TooltipContents: TooltipContents, ...props });
104
+ });
105
+ export default WiggleTooltip;
106
+ export { Tooltip };
107
+ //# sourceMappingURL=Tooltip.js.map
@@ -0,0 +1 @@
1
+ {"version":3,"file":"Tooltip.js","sourceRoot":"","sources":["../../../src/LinearWiggleDisplay/components/Tooltip.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,OAAO,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAChD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,KAAK,EAAE,MAAM,EAAE,MAAM,eAAe,CAAA;AAC7C,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAG1C,SAAS;AACT,OAAO,EAAE,sBAAsB,EAAE,MAAM,iBAAiB,CAAA;AACxD,OAAO,EAAE,SAAS,EAAE,MAAM,cAAc,CAAA;AAExC,2DAA2D;AAC3D,SAAS,GAAG,CAAC,CAAC,GAAG,CAAC;IAChB,OAAO,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;AAC7B,CAAC;AAED,SAAS,KAAK,CAAC,KAAa;IAC1B,OAAO,IAAI,CAAC,KAAK,CAAC,KAAK,GAAG,GAAG,CAAC,GAAG,GAAG,CAAA;AACtC,CAAC;AAED,MAAM,EAAE,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,CAAC,CAAC,cAAc,CAAC,OAAO,CAAC,CAAA;AAEnD,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,yBAAyB;IACzB,iGAAiG;IACjG,OAAO,EAAE;QACP,QAAQ,EAAE,UAAU;QACpB,aAAa,EAAE,MAAM;QACrB,eAAe,EAAE,KAAK,CAAC,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,GAAG,CAAC;QACpD,YAAY,EAAE,KAAK,CAAC,KAAK,CAAC,YAAY;QACtC,KAAK,EAAE,KAAK,CAAC,OAAO,CAAC,MAAM,CAAC,KAAK;QACjC,UAAU,EAAE,KAAK,CAAC,UAAU,CAAC,UAAU;QACvC,OAAO,EAAE,SAAS;QAClB,QAAQ,EAAE,KAAK,CAAC,UAAU,CAAC,OAAO,CAAC,EAAE,CAAC;QACtC,UAAU,EAAE,GAAG,KAAK,CAAC,EAAE,GAAG,EAAE,CAAC,IAAI;QACjC,QAAQ,EAAE,GAAG;QACb,QAAQ,EAAE,YAAY;KACvB;IAED,aAAa,EAAE;QACb,UAAU,EAAE,MAAM;QAClB,MAAM,EAAE,MAAM;QACd,KAAK,EAAE,CAAC;QACR,MAAM,EAAE,MAAM;QACd,GAAG,EAAE,sBAAsB;QAC3B,MAAM,EAAE,SAAS;QACjB,QAAQ,EAAE,UAAU;QACpB,aAAa,EAAE,MAAM;KACtB;CACF,CAAC,CAAC,CAAA;AAEH,MAAM,eAAe,GAAG,KAAK,CAAC,UAAU,CACtC,CAAC,EAAE,OAAO,EAAwB,EAAE,GAAG,EAAE,EAAE;IACzC,MAAM,KAAK,GAAG,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;IAClC,MAAM,GAAG,GAAG,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;IAC9B,MAAM,IAAI,GAAG,OAAO,CAAC,GAAG,CAAC,SAAS,CAAC,CAAA;IACnC,MAAM,GAAG,GAAG,CAAC,IAAI,EAAE,KAAK,KAAK,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,GAAG,EAAE,CAAC,KAAK,CAAC,KAAK,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC;SACvE,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;SAChB,IAAI,CAAC,GAAG,CAAC,CAAA;IAEZ,OAAO,OAAO,CAAC,GAAG,CAAC,SAAS,CAAC,KAAK,SAAS,CAAC,CAAC,CAAC,CAC5C,6BAAK,GAAG,EAAE,GAAG;QACV,GAAG;QACJ,+BAAM;;QACA,GAAG,CAAC,OAAO,CAAC,GAAG,CAAC,UAAU,CAAC,CAAC;QAClC,+BAAM;;QACA,GAAG,CAAC,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC;QAC/B,+BAAM;;QACA,GAAG,CAAC,OAAO,CAAC,GAAG,CAAC,UAAU,CAAC,CAAC,CAC9B,CACP,CAAC,CAAC,CAAC,CACF,6BAAK,GAAG,EAAE,GAAG;QACV,GAAG;QACJ,+BAAM;QACL,GAAG,GAAG,CAAC,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,EAAE,CAC3B,CACP,CAAA;AACH,CAAC,CACF,CAAA;AAID,MAAM,OAAO,GAAG,QAAQ,CACtB,CAAC,EACC,KAAK,EACL,MAAM,EACN,gBAAgB,EAChB,gBAAgB,EAChB,UAAU,EACV,eAAe,GAUhB,EAAE,EAAE;IACH,MAAM,EAAE,iBAAiB,EAAE,GAAG,KAAK,CAAA;IACnC,MAAM,CAAC,KAAK,EAAE,QAAQ,CAAC,GAAG,QAAQ,CAAC,CAAC,CAAC,CAAA;IACrC,MAAM,CAAC,QAAQ,EAAE,WAAW,CAAC,GAAG,QAAQ,CAAwB,IAAI,CAAC,CAAA;IACrE,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAE/B,4EAA4E;IAC5E,MAAM,WAAW,GAAG,OAAO,CACzB,GAAG,EAAE,CAAC,CAAC;QACL,qBAAqB,EAAE,GAAG,EAAE;YAC1B,MAAM,CAAC,GAAG,gBAAgB,CAAC,CAAC,CAAC,GAAG,KAAK,GAAG,CAAC,GAAG,EAAE,CAAA;YAC9C,MAAM,CAAC,GAAG,CAAA,UAAU,aAAV,UAAU,uBAAV,UAAU,CAAE,GAAG,KAAI,CAAC,CAAA;YAC9B,OAAO;gBACL,GAAG,EAAE,CAAC;gBACN,IAAI,EAAE,CAAC;gBACP,MAAM,EAAE,CAAC;gBACT,KAAK,EAAE,CAAC;gBACR,KAAK,EAAE,CAAC;gBACR,MAAM,EAAE,CAAC;gBACT,CAAC;gBACD,CAAC;gBACD,MAAM,KAAI,CAAC;aACZ,CAAA;QACH,CAAC;KACF,CAAC,EACF,CAAC,UAAU,aAAV,UAAU,uBAAV,UAAU,CAAE,GAAG,EAAE,gBAAgB,EAAE,KAAK,CAAC,CAC3C,CAAA;IACD,MAAM,EAAE,MAAM,EAAE,UAAU,EAAE,GAAG,SAAS,CAAC,WAAW,EAAE,QAAQ,CAAC,CAAA;IAE/D,OAAO,iBAAiB,CAAC,CAAC,CAAC,CACzB;QACE,oBAAC,MAAM;YACL,6BACE,GAAG,EAAE,WAAW,EAChB,SAAS,EAAE,OAAO,CAAC,OAAO;gBAC1B,yCAAyC;gBACzC,KAAK,EAAE,EAAE,GAAG,MAAM,CAAC,MAAM,EAAE,MAAM,EAAE,MAAM,EAAE,KACvC,UAAU,CAAC,MAAM;gBAErB,oBAAC,eAAe,IACd,GAAG,EAAE,CAAC,GAAmB,EAAE,EAAE;wBAC3B,QAAQ,CAAC,CAAA,GAAG,aAAH,GAAG,uBAAH,GAAG,CAAE,qBAAqB,GAAG,KAAK,KAAI,CAAC,CAAC,CAAA;oBACnD,CAAC,EACD,OAAO,EAAE,iBAAiB,GAC1B,CACE,CACC;QAET,6BACE,SAAS,EAAE,OAAO,CAAC,aAAa,EAChC,KAAK,EAAE;gBACL,IAAI,EAAE,gBAAgB,CAAC,CAAC,CAAC;gBACzB,MAAM,EAAE,MAAM,GAAG,sBAAsB,GAAG,CAAC;aAC5C,GACD,CACD,CACJ,CAAC,CAAC,CAAC,IAAI,CAAA;AACV,CAAC,CACF,CAAA;AAED,MAAM,aAAa,GAAG,QAAQ,CAC5B,CAAC,KAMA,EAAE,EAAE;IACH,OAAO,oBAAC,OAAO,IAAC,eAAe,EAAE,eAAe,KAAM,KAAK,GAAI,CAAA;AACjE,CAAC,CACF,CAAA;AACD,eAAe,aAAa,CAAA;AAC5B,OAAO,EAAE,OAAO,EAAE,CAAA"}
@@ -0,0 +1,8 @@
1
+ /// <reference types="react" />
2
+ import { WiggleDisplayModel } from '../models/model';
3
+ import YScaleBar from './YScaleBar';
4
+ declare const LinearWiggleDisplay: (props: {
5
+ model: WiggleDisplayModel;
6
+ }) => JSX.Element;
7
+ export default LinearWiggleDisplay;
8
+ export { YScaleBar };
@@ -0,0 +1,29 @@
1
+ import React from 'react';
2
+ import { measureText, getContainingView, getContainingTrack, } from '@jbrowse/core/util';
3
+ import { getConf } from '@jbrowse/core/configuration';
4
+ import { BaseLinearDisplayComponent, } from '@jbrowse/plugin-linear-genome-view';
5
+ import { observer } from 'mobx-react';
6
+ import YScaleBar from './YScaleBar';
7
+ const LinearWiggleDisplay = observer((props) => {
8
+ const { model } = props;
9
+ const { stats, height, needsScalebar } = model;
10
+ const { trackLabels } = getContainingView(model);
11
+ const track = getContainingTrack(model);
12
+ const left = trackLabels === 'overlapping'
13
+ ? measureText(getConf(track, 'name'), 12.8) + 100
14
+ : 50;
15
+ return (React.createElement("div", null,
16
+ React.createElement(BaseLinearDisplayComponent, { ...props }),
17
+ stats && needsScalebar ? (React.createElement("svg", { style: {
18
+ position: 'absolute',
19
+ top: 0,
20
+ left,
21
+ pointerEvents: 'none',
22
+ height,
23
+ width: 50,
24
+ } },
25
+ React.createElement(YScaleBar, { model: model }))) : null));
26
+ });
27
+ export default LinearWiggleDisplay;
28
+ export { YScaleBar };
29
+ //# sourceMappingURL=WiggleDisplayComponent.js.map
@@ -0,0 +1 @@
1
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@@ -0,0 +1,7 @@
1
+ /// <reference types="react" />
2
+ import { WiggleDisplayModel } from '../models/model';
3
+ declare const YScaleBar: ({ model, orientation, }: {
4
+ model: WiggleDisplayModel;
5
+ orientation?: string | undefined;
6
+ }) => JSX.Element | null;
7
+ export default YScaleBar;
@@ -0,0 +1,9 @@
1
+ import React from 'react';
2
+ import { observer } from 'mobx-react';
3
+ import { Axis, LEFT, RIGHT } from 'react-d3-axis-mod';
4
+ const YScaleBar = observer(({ model, orientation, }) => {
5
+ const { ticks } = model;
6
+ return ticks ? (React.createElement(Axis, { ...ticks, shadow: 2, format: (n) => n, style: { orient: orientation === 'left' ? LEFT : RIGHT } })) : null;
7
+ });
8
+ export default YScaleBar;
9
+ //# sourceMappingURL=YScaleBar.js.map
@@ -0,0 +1 @@
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@@ -0,0 +1,3 @@
1
+ export { default as configSchemaFactory } from './models/configSchema';
2
+ export { default as modelFactory, YSCALEBAR_LABEL_OFFSET } from './models/model';
3
+ export { default as ReactComponent } from './components/WiggleDisplayComponent';
@@ -0,0 +1,4 @@
1
+ export { default as configSchemaFactory } from './models/configSchema';
2
+ export { default as modelFactory, YSCALEBAR_LABEL_OFFSET } from './models/model';
3
+ export { default as ReactComponent } from './components/WiggleDisplayComponent';
4
+ //# sourceMappingURL=index.js.map
@@ -0,0 +1 @@
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+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearWiggleDisplay/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,mBAAmB,EAAE,MAAM,uBAAuB,CAAA;AACtE,OAAO,EAAE,OAAO,IAAI,YAAY,EAAE,sBAAsB,EAAE,MAAM,gBAAgB,CAAA;AAChF,OAAO,EAAE,OAAO,IAAI,cAAc,EAAE,MAAM,qCAAqC,CAAA"}
@@ -0,0 +1,2 @@
1
+ import PluginManager from '@jbrowse/core/PluginManager';
2
+ export default function WiggleConfigFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
@@ -0,0 +1,64 @@
1
+ import { ConfigurationSchema } from '@jbrowse/core/configuration';
2
+ import { baseLinearDisplayConfigSchema } from '@jbrowse/plugin-linear-genome-view';
3
+ import { types } from 'mobx-state-tree';
4
+ export default function WiggleConfigFactory(pluginManager) {
5
+ const XYPlotRendererConfigSchema = pluginManager.getRendererType('XYPlotRenderer').configSchema;
6
+ const DensityRendererConfigSchema = pluginManager.getRendererType('DensityRenderer').configSchema;
7
+ const LinePlotRendererConfigSchema = pluginManager.getRendererType('LinePlotRenderer').configSchema;
8
+ return ConfigurationSchema('LinearWiggleDisplay', {
9
+ autoscale: {
10
+ type: 'stringEnum',
11
+ defaultValue: 'local',
12
+ model: types.enumeration('Autoscale type', [
13
+ 'global',
14
+ 'local',
15
+ 'globalsd',
16
+ 'localsd',
17
+ 'zscore',
18
+ ]),
19
+ description: 'global/local using their min/max values or w/ standard deviations (globalsd/localsd)',
20
+ },
21
+ minimalTicks: {
22
+ type: 'boolean',
23
+ defaultValue: false,
24
+ description: 'use the minimal amount of ticks',
25
+ },
26
+ minScore: {
27
+ type: 'number',
28
+ defaultValue: Number.MIN_VALUE,
29
+ description: 'minimum value for the y-scale',
30
+ },
31
+ maxScore: {
32
+ type: 'number',
33
+ description: 'maximum value for the y-scale',
34
+ defaultValue: Number.MAX_VALUE,
35
+ },
36
+ numStdDev: {
37
+ type: 'number',
38
+ description: 'number of standard deviations to use for autoscale types globalsd or localsd',
39
+ defaultValue: 3,
40
+ },
41
+ scaleType: {
42
+ type: 'stringEnum',
43
+ model: types.enumeration('Scale type', ['linear', 'log']),
44
+ description: 'The type of scale to use',
45
+ defaultValue: 'linear',
46
+ },
47
+ inverted: {
48
+ type: 'boolean',
49
+ description: 'draw upside down',
50
+ defaultValue: false,
51
+ },
52
+ defaultRendering: {
53
+ type: 'stringEnum',
54
+ model: types.enumeration('Rendering', ['density', 'xyplot', 'line']),
55
+ defaultValue: 'xyplot',
56
+ },
57
+ renderers: ConfigurationSchema('RenderersConfiguration', {
58
+ DensityRenderer: DensityRendererConfigSchema,
59
+ XYPlotRenderer: XYPlotRendererConfigSchema,
60
+ LinePlotRenderer: LinePlotRendererConfigSchema,
61
+ }),
62
+ }, { baseConfiguration: baseLinearDisplayConfigSchema, explicitlyTyped: true });
63
+ }
64
+ //# sourceMappingURL=configSchema.js.map
@@ -0,0 +1 @@
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