@jbrowse/plugin-alignments 2.2.0 → 2.2.2

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Files changed (210) hide show
  1. package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js +12 -13
  2. package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js.map +1 -1
  3. package/dist/BamAdapter/BamAdapter.d.ts +1 -1
  4. package/dist/BamAdapter/BamAdapter.js +1 -0
  5. package/dist/BamAdapter/BamAdapter.js.map +1 -1
  6. package/dist/BamAdapter/BamSlightlyLazyFeature.js +1 -0
  7. package/dist/BamAdapter/BamSlightlyLazyFeature.js.map +1 -1
  8. package/dist/BamAdapter/MismatchParser.d.ts +2 -2
  9. package/dist/BamAdapter/MismatchParser.js +4 -7
  10. package/dist/BamAdapter/MismatchParser.js.map +1 -1
  11. package/dist/BamAdapter/configSchema.js +1 -1
  12. package/dist/BamAdapter/configSchema.js.map +1 -1
  13. package/dist/BamAdapter/index.js +7 -5
  14. package/dist/BamAdapter/index.js.map +1 -1
  15. package/dist/CramAdapter/CramSlightlyLazyFeature.d.ts +1 -10
  16. package/dist/CramAdapter/CramSlightlyLazyFeature.js +5 -218
  17. package/dist/CramAdapter/CramSlightlyLazyFeature.js.map +1 -1
  18. package/dist/CramAdapter/CramTestAdapters.d.ts +1 -1
  19. package/dist/CramAdapter/CramTestAdapters.js +3 -2
  20. package/dist/CramAdapter/CramTestAdapters.js.map +1 -1
  21. package/dist/CramAdapter/configSchema.js +2 -2
  22. package/dist/CramAdapter/configSchema.js.map +1 -1
  23. package/dist/CramAdapter/index.js +7 -5
  24. package/dist/CramAdapter/index.js.map +1 -1
  25. package/dist/CramAdapter/util.d.ts +18 -0
  26. package/dist/CramAdapter/util.js +241 -0
  27. package/dist/CramAdapter/util.js.map +1 -0
  28. package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.js +1 -1
  29. package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.js.map +1 -1
  30. package/dist/LinearAlignmentsDisplay/models/configSchema.d.ts +1 -1
  31. package/dist/LinearAlignmentsDisplay/models/model.d.ts +5 -5
  32. package/dist/LinearAlignmentsDisplay/models/model.js +7 -7
  33. package/dist/LinearAlignmentsDisplay/models/model.js.map +1 -1
  34. package/dist/LinearPileupDisplay/components/ColorByModifications.d.ts +3 -1
  35. package/dist/LinearPileupDisplay/components/ColorByModifications.js +7 -22
  36. package/dist/LinearPileupDisplay/components/ColorByModifications.js.map +1 -1
  37. package/dist/LinearPileupDisplay/components/ColorByTag.js +2 -22
  38. package/dist/LinearPileupDisplay/components/ColorByTag.js.map +1 -1
  39. package/dist/LinearPileupDisplay/components/FilterByTag.js +2 -15
  40. package/dist/LinearPileupDisplay/components/FilterByTag.js.map +1 -1
  41. package/dist/LinearPileupDisplay/components/SetFeatureHeight.js +2 -19
  42. package/dist/LinearPileupDisplay/components/SetFeatureHeight.js.map +1 -1
  43. package/dist/LinearPileupDisplay/components/SetMaxHeight.js +2 -18
  44. package/dist/LinearPileupDisplay/components/SetMaxHeight.js.map +1 -1
  45. package/dist/LinearPileupDisplay/components/SortByTag.js +2 -23
  46. package/dist/LinearPileupDisplay/components/SortByTag.js.map +1 -1
  47. package/dist/LinearPileupDisplay/configSchema.d.ts +4 -4
  48. package/dist/LinearPileupDisplay/configSchema.js +2 -2
  49. package/dist/LinearPileupDisplay/configSchema.js.map +1 -1
  50. package/dist/LinearPileupDisplay/index.d.ts +3 -0
  51. package/dist/LinearPileupDisplay/index.js +3 -0
  52. package/dist/LinearPileupDisplay/index.js.map +1 -1
  53. package/dist/LinearPileupDisplay/model.d.ts +19 -9
  54. package/dist/LinearPileupDisplay/model.js +25 -30
  55. package/dist/LinearPileupDisplay/model.js.map +1 -1
  56. package/dist/LinearSNPCoverageDisplay/components/Tooltip.d.ts +1 -1
  57. package/dist/LinearSNPCoverageDisplay/models/model.d.ts +14 -10
  58. package/dist/LinearSNPCoverageDisplay/models/model.js +8 -6
  59. package/dist/LinearSNPCoverageDisplay/models/model.js.map +1 -1
  60. package/dist/PileupRPC/rpcMethods.d.ts +1 -1
  61. package/dist/PileupRPC/rpcMethods.js +12 -7
  62. package/dist/PileupRPC/rpcMethods.js.map +1 -1
  63. package/dist/PileupRenderer/PileupLayoutSession.d.ts +1 -1
  64. package/dist/PileupRenderer/PileupRenderer.js +32 -28
  65. package/dist/PileupRenderer/PileupRenderer.js.map +1 -1
  66. package/dist/PileupRenderer/configSchema.js +1 -1
  67. package/dist/PileupRenderer/configSchema.js.map +1 -1
  68. package/dist/PileupRenderer/index.js +8 -6
  69. package/dist/PileupRenderer/index.js.map +1 -1
  70. package/dist/SNPCoverageAdapter/SNPCoverageAdapter.d.ts +0 -51
  71. package/dist/SNPCoverageAdapter/SNPCoverageAdapter.js +3 -182
  72. package/dist/SNPCoverageAdapter/SNPCoverageAdapter.js.map +1 -1
  73. package/dist/SNPCoverageAdapter/configSchema.d.ts +2 -3
  74. package/dist/SNPCoverageAdapter/configSchema.js +6 -3
  75. package/dist/SNPCoverageAdapter/configSchema.js.map +1 -1
  76. package/dist/SNPCoverageAdapter/generateCoverageBins.d.ts +53 -0
  77. package/dist/SNPCoverageAdapter/generateCoverageBins.js +185 -0
  78. package/dist/SNPCoverageAdapter/generateCoverageBins.js.map +1 -0
  79. package/dist/SNPCoverageAdapter/index.d.ts +1 -2
  80. package/dist/SNPCoverageAdapter/index.js +17 -14
  81. package/dist/SNPCoverageAdapter/index.js.map +1 -1
  82. package/dist/index.d.ts +3 -2
  83. package/dist/index.js +4 -2
  84. package/dist/index.js.map +1 -1
  85. package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js +12 -13
  86. package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js.map +1 -1
  87. package/esm/BamAdapter/BamAdapter.d.ts +1 -1
  88. package/esm/BamAdapter/BamAdapter.js +1 -0
  89. package/esm/BamAdapter/BamAdapter.js.map +1 -1
  90. package/esm/BamAdapter/BamSlightlyLazyFeature.js +1 -0
  91. package/esm/BamAdapter/BamSlightlyLazyFeature.js.map +1 -1
  92. package/esm/BamAdapter/MismatchParser.d.ts +2 -2
  93. package/esm/BamAdapter/MismatchParser.js +4 -7
  94. package/esm/BamAdapter/MismatchParser.js.map +1 -1
  95. package/esm/BamAdapter/configSchema.js +1 -1
  96. package/esm/BamAdapter/configSchema.js.map +1 -1
  97. package/esm/BamAdapter/index.js +7 -5
  98. package/esm/BamAdapter/index.js.map +1 -1
  99. package/esm/CramAdapter/CramSlightlyLazyFeature.d.ts +1 -10
  100. package/esm/CramAdapter/CramSlightlyLazyFeature.js +5 -218
  101. package/esm/CramAdapter/CramSlightlyLazyFeature.js.map +1 -1
  102. package/esm/CramAdapter/CramTestAdapters.d.ts +1 -1
  103. package/esm/CramAdapter/CramTestAdapters.js +3 -2
  104. package/esm/CramAdapter/CramTestAdapters.js.map +1 -1
  105. package/esm/CramAdapter/configSchema.js +2 -2
  106. package/esm/CramAdapter/configSchema.js.map +1 -1
  107. package/esm/CramAdapter/index.js +7 -5
  108. package/esm/CramAdapter/index.js.map +1 -1
  109. package/esm/CramAdapter/util.d.ts +18 -0
  110. package/esm/CramAdapter/util.js +236 -0
  111. package/esm/CramAdapter/util.js.map +1 -0
  112. package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.js +1 -1
  113. package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.js.map +1 -1
  114. package/esm/LinearAlignmentsDisplay/models/configSchema.d.ts +1 -1
  115. package/esm/LinearAlignmentsDisplay/models/model.d.ts +5 -5
  116. package/esm/LinearAlignmentsDisplay/models/model.js +7 -7
  117. package/esm/LinearAlignmentsDisplay/models/model.js.map +1 -1
  118. package/esm/LinearPileupDisplay/components/ColorByModifications.d.ts +3 -1
  119. package/esm/LinearPileupDisplay/components/ColorByModifications.js +8 -23
  120. package/esm/LinearPileupDisplay/components/ColorByModifications.js.map +1 -1
  121. package/esm/LinearPileupDisplay/components/ColorByTag.js +3 -20
  122. package/esm/LinearPileupDisplay/components/ColorByTag.js.map +1 -1
  123. package/esm/LinearPileupDisplay/components/FilterByTag.js +3 -13
  124. package/esm/LinearPileupDisplay/components/FilterByTag.js.map +1 -1
  125. package/esm/LinearPileupDisplay/components/SetFeatureHeight.js +3 -17
  126. package/esm/LinearPileupDisplay/components/SetFeatureHeight.js.map +1 -1
  127. package/esm/LinearPileupDisplay/components/SetMaxHeight.js +3 -16
  128. package/esm/LinearPileupDisplay/components/SetMaxHeight.js.map +1 -1
  129. package/esm/LinearPileupDisplay/components/SortByTag.js +3 -21
  130. package/esm/LinearPileupDisplay/components/SortByTag.js.map +1 -1
  131. package/esm/LinearPileupDisplay/configSchema.d.ts +4 -4
  132. package/esm/LinearPileupDisplay/configSchema.js +2 -2
  133. package/esm/LinearPileupDisplay/configSchema.js.map +1 -1
  134. package/esm/LinearPileupDisplay/index.d.ts +3 -0
  135. package/esm/LinearPileupDisplay/index.js +1 -0
  136. package/esm/LinearPileupDisplay/index.js.map +1 -1
  137. package/esm/LinearPileupDisplay/model.d.ts +19 -9
  138. package/esm/LinearPileupDisplay/model.js +25 -30
  139. package/esm/LinearPileupDisplay/model.js.map +1 -1
  140. package/esm/LinearSNPCoverageDisplay/components/Tooltip.d.ts +1 -1
  141. package/esm/LinearSNPCoverageDisplay/models/model.d.ts +14 -10
  142. package/esm/LinearSNPCoverageDisplay/models/model.js +9 -7
  143. package/esm/LinearSNPCoverageDisplay/models/model.js.map +1 -1
  144. package/esm/PileupRPC/rpcMethods.d.ts +1 -1
  145. package/esm/PileupRPC/rpcMethods.js +12 -7
  146. package/esm/PileupRPC/rpcMethods.js.map +1 -1
  147. package/esm/PileupRenderer/PileupLayoutSession.d.ts +1 -1
  148. package/esm/PileupRenderer/PileupRenderer.js +32 -28
  149. package/esm/PileupRenderer/PileupRenderer.js.map +1 -1
  150. package/esm/PileupRenderer/configSchema.js +1 -1
  151. package/esm/PileupRenderer/configSchema.js.map +1 -1
  152. package/esm/PileupRenderer/index.js +8 -6
  153. package/esm/PileupRenderer/index.js.map +1 -1
  154. package/esm/SNPCoverageAdapter/SNPCoverageAdapter.d.ts +0 -51
  155. package/esm/SNPCoverageAdapter/SNPCoverageAdapter.js +4 -183
  156. package/esm/SNPCoverageAdapter/SNPCoverageAdapter.js.map +1 -1
  157. package/esm/SNPCoverageAdapter/configSchema.d.ts +2 -3
  158. package/esm/SNPCoverageAdapter/configSchema.js +6 -3
  159. package/esm/SNPCoverageAdapter/configSchema.js.map +1 -1
  160. package/esm/SNPCoverageAdapter/generateCoverageBins.d.ts +53 -0
  161. package/esm/SNPCoverageAdapter/generateCoverageBins.js +182 -0
  162. package/esm/SNPCoverageAdapter/generateCoverageBins.js.map +1 -0
  163. package/esm/SNPCoverageAdapter/index.d.ts +1 -2
  164. package/esm/SNPCoverageAdapter/index.js +17 -15
  165. package/esm/SNPCoverageAdapter/index.js.map +1 -1
  166. package/esm/index.d.ts +3 -2
  167. package/esm/index.js +2 -2
  168. package/esm/index.js.map +1 -1
  169. package/package.json +4 -3
  170. package/src/AlignmentsFeatureDetail/AlignmentsFeatureDetail.tsx +17 -16
  171. package/src/AlignmentsFeatureDetail/__snapshots__/index.test.js.snap +1 -473
  172. package/src/AlignmentsFeatureDetail/index.test.js +6 -4
  173. package/src/BamAdapter/BamAdapter.ts +3 -2
  174. package/src/BamAdapter/BamSlightlyLazyFeature.ts +2 -1
  175. package/src/BamAdapter/MismatchParser.test.ts +21 -12
  176. package/src/BamAdapter/MismatchParser.ts +7 -10
  177. package/src/BamAdapter/__snapshots__/BamAdapter.test.ts.snap +135 -135
  178. package/src/BamAdapter/configSchema.ts +1 -1
  179. package/src/BamAdapter/index.ts +7 -8
  180. package/src/CombinationTest.test.ts +107 -0
  181. package/src/CramAdapter/CramSlightlyLazyFeature.ts +10 -219
  182. package/src/CramAdapter/CramTestAdapters.ts +2 -1
  183. package/src/CramAdapter/__snapshots__/CramAdapter.test.ts.snap +31 -31
  184. package/src/CramAdapter/__snapshots__/util.test.ts.snap +14 -0
  185. package/src/CramAdapter/configSchema.ts +2 -3
  186. package/src/CramAdapter/index.ts +7 -8
  187. package/src/CramAdapter/util.test.ts +26 -0
  188. package/src/CramAdapter/util.ts +251 -0
  189. package/src/LinearAlignmentsDisplay/components/AlignmentsDisplay.tsx +3 -1
  190. package/src/LinearAlignmentsDisplay/models/model.tsx +8 -7
  191. package/src/LinearPileupDisplay/components/ColorByModifications.tsx +5 -34
  192. package/src/LinearPileupDisplay/components/ColorByTag.tsx +2 -29
  193. package/src/LinearPileupDisplay/components/FilterByTag.tsx +2 -22
  194. package/src/LinearPileupDisplay/components/SetFeatureHeight.tsx +2 -22
  195. package/src/LinearPileupDisplay/components/SetMaxHeight.tsx +2 -24
  196. package/src/LinearPileupDisplay/components/SortByTag.tsx +2 -31
  197. package/src/LinearPileupDisplay/configSchema.ts +3 -5
  198. package/src/LinearPileupDisplay/index.ts +5 -0
  199. package/src/LinearPileupDisplay/model.ts +31 -30
  200. package/src/LinearSNPCoverageDisplay/models/model.ts +12 -8
  201. package/src/PileupRPC/rpcMethods.ts +15 -20
  202. package/src/PileupRenderer/{PileupRenderer.tsx → PileupRenderer.ts} +48 -54
  203. package/src/PileupRenderer/configSchema.ts +1 -1
  204. package/src/PileupRenderer/index.ts +8 -9
  205. package/src/SNPCoverageAdapter/SNPCoverageAdapter.ts +5 -249
  206. package/src/SNPCoverageAdapter/configSchema.ts +14 -13
  207. package/src/SNPCoverageAdapter/generateCoverageBins.ts +245 -0
  208. package/src/SNPCoverageAdapter/index.ts +17 -18
  209. package/src/__snapshots__/index.test.ts.snap +1 -1
  210. package/src/index.ts +11 -4
package/esm/LinearPileupDisplay/components/FilterByTag.js CHANGED
@@ -1,19 +1,13 @@
1
1
  import React, { useState } from 'react';
2
2
  import { observer } from 'mobx-react';
3
- import { Button, Dialog, DialogActions, DialogContent, DialogTitle, IconButton, Link, Paper, TextField, Typography, } from '@mui/material';
3
+ import { Button, DialogActions, DialogContent, Link, Paper, TextField, Typography, } from '@mui/material';
4
+ import { Dialog } from '@jbrowse/core/ui';
4
5
  import { makeStyles } from 'tss-react/mui';
5
- import CloseIcon from '@mui/icons-material/Close';
6
6
  const useStyles = makeStyles()(theme => ({
7
7
  paper: {
8
8
  padding: theme.spacing(2),
9
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  margin: theme.spacing(2),
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10
  },
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- closeButton: {
12
- position: 'absolute',
13
- right: theme.spacing(1),
14
- top: theme.spacing(1),
15
- color: theme.palette.grey[500],
16
- },
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  field: {
18
12
  margin: theme.spacing(2),
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13
  },
@@ -63,11 +57,7 @@ function FilterByTagDlg(props) {
63
57
  const [readName, setReadName] = useState((filterBy === null || filterBy === void 0 ? void 0 : filterBy.readName) || '');
64
58
  const validTag = tag.match(/^[A-Za-z][A-Za-z0-9]$/);
65
59
  const site = 'https://broadinstitute.github.io/picard/explain-flags.html';
66
- return (React.createElement(Dialog, { open: true, onClose: handleClose },
67
- React.createElement(DialogTitle, null,
68
- "Filter options",
69
- React.createElement(IconButton, { "aria-label": "close", className: classes.closeButton, onClick: handleClose },
70
- React.createElement(CloseIcon, null))),
60
+ return (React.createElement(Dialog, { open: true, onClose: handleClose, title: "Filter options" },
71
61
  React.createElement(DialogContent, null,
72
62
  React.createElement(Typography, null,
73
63
  "Set filter bitmask options. Refer to ",
package/esm/LinearPileupDisplay/components/FilterByTag.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"FilterByTag.js","sourceRoot":"","sources":["../../../src/LinearPileupDisplay/components/FilterByTag.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AACvC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EACL,MAAM,EACN,MAAM,EACN,aAAa,EACb,aAAa,EACb,WAAW,EACX,UAAU,EACV,IAAI,EACJ,KAAK,EACL,SAAS,EACT,UAAU,GACX,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,OAAO,SAAS,MAAM,2BAA2B,CAAA;AAEjD,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,KAAK,EAAE;QACL,OAAO,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;QACzB,MAAM,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;KACzB;IACD,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;IACD,KAAK,EAAE;QACL,MAAM,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;KACzB;CACF,CAAC,CAAC,CAAA;AAEH,MAAM,SAAS,GAAG;IAChB,aAAa;IACb,4BAA4B;IAC5B,eAAe;IACf,eAAe;IACf,qBAAqB;IACrB,qBAAqB;IACrB,eAAe;IACf,gBAAgB;IAChB,uBAAuB;IACvB,2CAA2C;IAC3C,kCAAkC;IAClC,yBAAyB;CAC1B,CAAA;AAED,SAAS,OAAO,CAAC,KAA2C;IAC1D,MAAM,EAAE,IAAI,GAAG,CAAC,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;IACnC,OAAO,CACL;QACE,oBAAC,SAAS,IACR,IAAI,EAAC,QAAQ,EACb,KAAK,EAAE,IAAI,EACX,QAAQ,EAAE,KAAK,CAAC,EAAE,CAAC,OAAO,CAAC,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,GAC/C;QACD,SAAS,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,KAAK,EAAE,EAAE;YAC7B,MAAM,GAAG,GAAG,IAAI,GAAG,CAAC,CAAC,IAAI,KAAK,CAAC,CAAA;YAC/B,MAAM,GAAG,GAAG,GAAG,IAAI,IAAI,GAAG,EAAE,CAAA;YAC5B,OAAO,CACL,6BAAK,GAAG,EAAE,GAAG;gBACX,+BACE,IAAI,EAAC,UAAU,EACf,OAAO,EAAE,OAAO,CAAC,GAAG,CAAC,EACrB,QAAQ,EAAE,KAAK,CAAC,EAAE;wBAChB,IAAI,KAAK,CAAC,MAAM,CAAC,OAAO,EAAE;4BACxB,OAAO,CAAC,IAAI,GAAG,CAAC,CAAC,IAAI,KAAK,CAAC,CAAC,CAAA;yBAC7B;6BAAM;4BACL,OAAO,CAAC,IAAI,GAAG,CAAC,CAAC,CAAC,IAAI,KAAK,CAAC,CAAC,CAAA;yBAC9B;oBACH,CAAC,GACD;gBACF,+BAAO,OAAO,EAAE,GAAG,IAAG,IAAI,CAAS,CAC/B,CACP,CAAA;QACH,CAAC,CAAC,CACD,CACJ,CAAA;AACH,CAAC;AAED,SAAS,cAAc,CAAC,KAWvB;;IACC,MAAM,EAAE,KAAK,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IACpC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,QAAQ,EAAE,GAAG,KAAK,CAAA;IAC1B,MAAM,CAAC,WAAW,EAAE,cAAc,CAAC,GAAG,QAAQ,CAAC,QAAQ,aAAR,QAAQ,uBAAR,QAAQ,CAAE,WAAW,CAAC,CAAA;IACrE,MAAM,CAAC,WAAW,EAAE,cAAc,CAAC,GAAG,QAAQ,CAAC,QAAQ,aAAR,QAAQ,uBAAR,QAAQ,CAAE,WAAW,CAAC,CAAA;IACrE,MAAM,CAAC,GAAG,EAAE,MAAM,CAAC,GAAG,QAAQ,CAAC,CAAA,MAAA,QAAQ,aAAR,QAAQ,uBAAR,QAAQ,CAAE,SAAS,0CAAE,GAAG,KAAI,EAAE,CAAC,CAAA;IAC9D,MAAM,CAAC,QAAQ,EAAE,WAAW,CAAC,GAAG,QAAQ,CAAC,CAAA,MAAA,QAAQ,aAAR,QAAQ,uBAAR,QAAQ,CAAE,SAAS,0CAAE,KAAK,KAAI,EAAE,CAAC,CAAA;IAC1E,MAAM,CAAC,QAAQ,EAAE,WAAW,CAAC,GAAG,QAAQ,CAAC,CAAA,QAAQ,aAAR,QAAQ,uBAAR,QAAQ,CAAE,QAAQ,KAAI,EAAE,CAAC,CAAA;IAClE,MAAM,QAAQ,GAAG,GAAG,CAAC,KAAK,CAAC,uBAAuB,CAAC,CAAA;IAEnD,MAAM,IAAI,GAAG,4DAA4D,CAAA;IAEzE,OAAO,CACL,oBAAC,MAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW;QAC/B,oBAAC,WAAW;;YAEV,oBAAC,UAAU,kBACE,OAAO,EAClB,SAAS,EAAE,OAAO,CAAC,WAAW,EAC9B,OAAO,EAAE,WAAW;gBAEpB,oBAAC,SAAS,OAAG,CACF,CACD;QACd,oBAAC,aAAa;YACZ,oBAAC,UAAU;;gBAC4B,oBAAC,IAAI,IAAC,IAAI,EAAE,IAAI,IAAG,IAAI,CAAQ;gBAAC,GAAG;8BAE7D;YACb,oBAAC,KAAK,IAAC,SAAS,EAAE,OAAO,CAAC,KAAK,EAAE,OAAO,EAAC,UAAU;gBACjD,6BAAK,KAAK,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE;oBAC7B;wBACE,oBAAC,UAAU,yCAA4C;wBACvD,oBAAC,OAAO,IAAC,IAAI,EAAE,WAAW,EAAE,OAAO,EAAE,cAAc,GAAI,CACnD;oBACN;wBACE,oBAAC,UAAU,6CAAgD;wBAC3D,oBAAC,OAAO,IAAC,IAAI,EAAE,WAAW,EAAE,OAAO,EAAE,cAAc,GAAI,CACnD,CACF,CACA;YACR,oBAAC,KAAK,IAAC,SAAS,EAAE,OAAO,CAAC,KAAK,EAAE,OAAO,EAAC,UAAU;gBACjD,oBAAC,UAAU,kQAKE;gBACb,oBAAC,SAAS,IACR,SAAS,EAAE,OAAO,CAAC,KAAK,EACxB,KAAK,EAAE,GAAG,EACV,QAAQ,EAAE,KAAK,CAAC,EAAE;wBAChB,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;oBAC5B,CAAC,EACD,WAAW,EAAC,gBAAgB,EAC5B,UAAU,EAAE;wBACV,SAAS,EAAE,CAAC;wBACZ,aAAa,EAAE,sBAAsB;qBACtC,EACD,KAAK,EAAE,GAAG,CAAC,MAAM,KAAK,CAAC,IAAI,CAAC,QAAQ,EACpC,UAAU,EAAE,GAAG,CAAC,MAAM,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAC,iBAAiB,CAAC,CAAC,CAAC,EAAE,iBACtD,gBAAgB,GAC5B;gBACF,oBAAC,SAAS,IACR,SAAS,EAAE,OAAO,CAAC,KAAK,EACxB,KAAK,EAAE,QAAQ,EACf,QAAQ,EAAE,KAAK,CAAC,EAAE;wBAChB,WAAW,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;oBACjC,CAAC,EACD,WAAW,EAAC,iBAAiB,EAC7B,UAAU,EAAE;wBACV,aAAa,EAAE,sBAAsB;qBACtC,iBACW,iBAAiB,GAC7B,CACI;YACR,oBAAC,KAAK,IAAC,SAAS,EAAE,OAAO,CAAC,KAAK,EAAE,OAAO,EAAC,UAAU;gBACjD,oBAAC,UAAU,8BAAiC;gBAC5C,oBAAC,SAAS,IACR,SAAS,EAAE,OAAO,CAAC,KAAK,EACxB,KAAK,EAAE,QAAQ,EACf,QAAQ,EAAE,KAAK,CAAC,EAAE;wBAChB,WAAW,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;oBACjC,CAAC,EACD,WAAW,EAAC,iBAAiB,EAC7B,UAAU,EAAE;wBACV,aAAa,EAAE,0BAA0B;qBAC1C,iBACW,oBAAoB,GAChC,CACI;YACR,oBAAC,aAAa;gBACZ,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,SAAS,QACT,IAAI,EAAC,QAAQ,EACb,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,WAAW,CAAC;4BAChB,WAAW;4BACX,WAAW;4BACX,QAAQ;4BACR,SAAS,EACP,GAAG,KAAK,EAAE;gCACR,CAAC,CAAC;oCACE,GAAG;oCACH,KAAK,EAAE,QAAQ;iCAChB;gCACH,CAAC,CAAC,SAAS;yBAChB,CAAC,CAAA;wBACF,WAAW,EAAE,CAAA;oBACf,CAAC,aAGM;gBACT,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,WAAW,EACjB,OAAO,EAAE,GAAG,EAAE,CAAC,WAAW,EAAE,aAGrB,CACK,CACF,CACT,CACV,CAAA;AACH,CAAC;AAED,eAAe,QAAQ,CAAC,cAAc,CAAC,CAAA"}
1
+ {"version":3,"file":"FilterByTag.js","sourceRoot":"","sources":["../../../src/LinearPileupDisplay/components/FilterByTag.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AACvC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EACL,MAAM,EACN,aAAa,EACb,aAAa,EACb,IAAI,EACJ,KAAK,EACL,SAAS,EACT,UAAU,GACX,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;AACzC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,KAAK,EAAE;QACL,OAAO,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;QACzB,MAAM,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;KACzB;IACD,KAAK,EAAE;QACL,MAAM,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;KACzB;CACF,CAAC,CAAC,CAAA;AAEH,MAAM,SAAS,GAAG;IAChB,aAAa;IACb,4BAA4B;IAC5B,eAAe;IACf,eAAe;IACf,qBAAqB;IACrB,qBAAqB;IACrB,eAAe;IACf,gBAAgB;IAChB,uBAAuB;IACvB,2CAA2C;IAC3C,kCAAkC;IAClC,yBAAyB;CAC1B,CAAA;AAED,SAAS,OAAO,CAAC,KAA2C;IAC1D,MAAM,EAAE,IAAI,GAAG,CAAC,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;IACnC,OAAO,CACL;QACE,oBAAC,SAAS,IACR,IAAI,EAAC,QAAQ,EACb,KAAK,EAAE,IAAI,EACX,QAAQ,EAAE,KAAK,CAAC,EAAE,CAAC,OAAO,CAAC,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,GAC/C;QACD,SAAS,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,KAAK,EAAE,EAAE;YAC7B,MAAM,GAAG,GAAG,IAAI,GAAG,CAAC,CAAC,IAAI,KAAK,CAAC,CAAA;YAC/B,MAAM,GAAG,GAAG,GAAG,IAAI,IAAI,GAAG,EAAE,CAAA;YAC5B,OAAO,CACL,6BAAK,GAAG,EAAE,GAAG;gBACX,+BACE,IAAI,EAAC,UAAU,EACf,OAAO,EAAE,OAAO,CAAC,GAAG,CAAC,EACrB,QAAQ,EAAE,KAAK,CAAC,EAAE;wBAChB,IAAI,KAAK,CAAC,MAAM,CAAC,OAAO,EAAE;4BACxB,OAAO,CAAC,IAAI,GAAG,CAAC,CAAC,IAAI,KAAK,CAAC,CAAC,CAAA;yBAC7B;6BAAM;4BACL,OAAO,CAAC,IAAI,GAAG,CAAC,CAAC,CAAC,IAAI,KAAK,CAAC,CAAC,CAAA;yBAC9B;oBACH,CAAC,GACD;gBACF,+BAAO,OAAO,EAAE,GAAG,IAAG,IAAI,CAAS,CAC/B,CACP,CAAA;QACH,CAAC,CAAC,CACD,CACJ,CAAA;AACH,CAAC;AAED,SAAS,cAAc,CAAC,KAWvB;;IACC,MAAM,EAAE,KAAK,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IACpC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,QAAQ,EAAE,GAAG,KAAK,CAAA;IAC1B,MAAM,CAAC,WAAW,EAAE,cAAc,CAAC,GAAG,QAAQ,CAAC,QAAQ,aAAR,QAAQ,uBAAR,QAAQ,CAAE,WAAW,CAAC,CAAA;IACrE,MAAM,CAAC,WAAW,EAAE,cAAc,CAAC,GAAG,QAAQ,CAAC,QAAQ,aAAR,QAAQ,uBAAR,QAAQ,CAAE,WAAW,CAAC,CAAA;IACrE,MAAM,CAAC,GAAG,EAAE,MAAM,CAAC,GAAG,QAAQ,CAAC,CAAA,MAAA,QAAQ,aAAR,QAAQ,uBAAR,QAAQ,CAAE,SAAS,0CAAE,GAAG,KAAI,EAAE,CAAC,CAAA;IAC9D,MAAM,CAAC,QAAQ,EAAE,WAAW,CAAC,GAAG,QAAQ,CAAC,CAAA,MAAA,QAAQ,aAAR,QAAQ,uBAAR,QAAQ,CAAE,SAAS,0CAAE,KAAK,KAAI,EAAE,CAAC,CAAA;IAC1E,MAAM,CAAC,QAAQ,EAAE,WAAW,CAAC,GAAG,QAAQ,CAAC,CAAA,QAAQ,aAAR,QAAQ,uBAAR,QAAQ,CAAE,QAAQ,KAAI,EAAE,CAAC,CAAA;IAClE,MAAM,QAAQ,GAAG,GAAG,CAAC,KAAK,CAAC,uBAAuB,CAAC,CAAA;IAEnD,MAAM,IAAI,GAAG,4DAA4D,CAAA;IAEzE,OAAO,CACL,oBAAC,MAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW,EAAE,KAAK,EAAC,gBAAgB;QACvD,oBAAC,aAAa;YACZ,oBAAC,UAAU;;gBAC4B,oBAAC,IAAI,IAAC,IAAI,EAAE,IAAI,IAAG,IAAI,CAAQ;gBAAC,GAAG;8BAE7D;YACb,oBAAC,KAAK,IAAC,SAAS,EAAE,OAAO,CAAC,KAAK,EAAE,OAAO,EAAC,UAAU;gBACjD,6BAAK,KAAK,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE;oBAC7B;wBACE,oBAAC,UAAU,yCAA4C;wBACvD,oBAAC,OAAO,IAAC,IAAI,EAAE,WAAW,EAAE,OAAO,EAAE,cAAc,GAAI,CACnD;oBACN;wBACE,oBAAC,UAAU,6CAAgD;wBAC3D,oBAAC,OAAO,IAAC,IAAI,EAAE,WAAW,EAAE,OAAO,EAAE,cAAc,GAAI,CACnD,CACF,CACA;YACR,oBAAC,KAAK,IAAC,SAAS,EAAE,OAAO,CAAC,KAAK,EAAE,OAAO,EAAC,UAAU;gBACjD,oBAAC,UAAU,kQAKE;gBACb,oBAAC,SAAS,IACR,SAAS,EAAE,OAAO,CAAC,KAAK,EACxB,KAAK,EAAE,GAAG,EACV,QAAQ,EAAE,KAAK,CAAC,EAAE;wBAChB,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;oBAC5B,CAAC,EACD,WAAW,EAAC,gBAAgB,EAC5B,UAAU,EAAE;wBACV,SAAS,EAAE,CAAC;wBACZ,aAAa,EAAE,sBAAsB;qBACtC,EACD,KAAK,EAAE,GAAG,CAAC,MAAM,KAAK,CAAC,IAAI,CAAC,QAAQ,EACpC,UAAU,EAAE,GAAG,CAAC,MAAM,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAC,iBAAiB,CAAC,CAAC,CAAC,EAAE,iBACtD,gBAAgB,GAC5B;gBACF,oBAAC,SAAS,IACR,SAAS,EAAE,OAAO,CAAC,KAAK,EACxB,KAAK,EAAE,QAAQ,EACf,QAAQ,EAAE,KAAK,CAAC,EAAE;wBAChB,WAAW,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;oBACjC,CAAC,EACD,WAAW,EAAC,iBAAiB,EAC7B,UAAU,EAAE;wBACV,aAAa,EAAE,sBAAsB;qBACtC,iBACW,iBAAiB,GAC7B,CACI;YACR,oBAAC,KAAK,IAAC,SAAS,EAAE,OAAO,CAAC,KAAK,EAAE,OAAO,EAAC,UAAU;gBACjD,oBAAC,UAAU,8BAAiC;gBAC5C,oBAAC,SAAS,IACR,SAAS,EAAE,OAAO,CAAC,KAAK,EACxB,KAAK,EAAE,QAAQ,EACf,QAAQ,EAAE,KAAK,CAAC,EAAE;wBAChB,WAAW,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;oBACjC,CAAC,EACD,WAAW,EAAC,iBAAiB,EAC7B,UAAU,EAAE;wBACV,aAAa,EAAE,0BAA0B;qBAC1C,iBACW,oBAAoB,GAChC,CACI;YACR,oBAAC,aAAa;gBACZ,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,SAAS,QACT,IAAI,EAAC,QAAQ,EACb,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,WAAW,CAAC;4BAChB,WAAW;4BACX,WAAW;4BACX,QAAQ;4BACR,SAAS,EACP,GAAG,KAAK,EAAE;gCACR,CAAC,CAAC;oCACE,GAAG;oCACH,KAAK,EAAE,QAAQ;iCAChB;gCACH,CAAC,CAAC,SAAS;yBAChB,CAAC,CAAA;wBACF,WAAW,EAAE,CAAA;oBACf,CAAC,aAGM;gBACT,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,WAAW,EACjB,OAAO,EAAE,GAAG,EAAE,CAAC,WAAW,EAAE,aAGrB,CACK,CACF,CACT,CACV,CAAA;AACH,CAAC;AAED,eAAe,QAAQ,CAAC,cAAc,CAAC,CAAA"}
package/esm/LinearPileupDisplay/components/SetFeatureHeight.js CHANGED
@@ -1,28 +1,14 @@
1
1
  import React, { useState } from 'react';
2
2
  import { observer } from 'mobx-react';
3
- import { Button, Checkbox, Dialog, DialogActions, DialogContent, DialogTitle, FormControlLabel, IconButton, TextField, Typography, } from '@mui/material';
4
- import { makeStyles } from 'tss-react/mui';
5
- import CloseIcon from '@mui/icons-material/Close';
6
- const useStyles = makeStyles()(theme => ({
7
- closeButton: {
8
- position: 'absolute',
9
- right: theme.spacing(1),
10
- top: theme.spacing(1),
11
- color: theme.palette.grey[500],
12
- },
13
- }));
3
+ import { Button, Checkbox, DialogActions, DialogContent, FormControlLabel, TextField, Typography, } from '@mui/material';
4
+ import { Dialog } from '@jbrowse/core/ui';
14
5
  function SetFeatureHeightDlg(props) {
15
- const { classes } = useStyles();
16
6
  const { model, handleClose } = props;
17
7
  const { featureHeightSetting, noSpacing: noSpacingSetting } = model;
18
8
  const [height, setHeight] = useState(`${featureHeightSetting}`);
19
9
  const [noSpacing, setNoSpacing] = useState(noSpacingSetting);
20
10
  const ok = height !== '' && !Number.isNaN(+height);
21
- return (React.createElement(Dialog, { open: true, onClose: handleClose },
22
- React.createElement(DialogTitle, null,
23
- "Set feature height",
24
- React.createElement(IconButton, { className: classes.closeButton, onClick: handleClose },
25
- React.createElement(CloseIcon, null))),
11
+ return (React.createElement(Dialog, { open: true, onClose: handleClose, title: 'Set feature height' },
26
12
  React.createElement(DialogContent, null,
27
13
  React.createElement(Typography, null, "Adjust the feature height and whether there is any spacing between features. Setting feature height to 1 and removing spacing makes the display very compact."),
28
14
  React.createElement(TextField, { value: height, helperText: "Feature height", onChange: event => {
package/esm/LinearPileupDisplay/components/SetFeatureHeight.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"SetFeatureHeight.js","sourceRoot":"","sources":["../../../src/LinearPileupDisplay/components/SetFeatureHeight.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AACvC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EACL,MAAM,EACN,QAAQ,EACR,MAAM,EACN,aAAa,EACb,aAAa,EACb,WAAW,EACX,gBAAgB,EAChB,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,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,SAAS,mBAAmB,CAAC,KAQ5B;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,KAAK,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IACpC,MAAM,EAAE,oBAAoB,EAAE,SAAS,EAAE,gBAAgB,EAAE,GAAG,KAAK,CAAA;IACnE,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,QAAQ,CAAC,GAAG,oBAAoB,EAAE,CAAC,CAAA;IAC/D,MAAM,CAAC,SAAS,EAAE,YAAY,CAAC,GAAG,QAAQ,CAAC,gBAAgB,CAAC,CAAA;IAE5D,MAAM,EAAE,GAAG,MAAM,KAAK,EAAE,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,MAAM,CAAC,CAAA;IAElD,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;YACZ,oBAAC,UAAU,wKAIE;YACb,oBAAC,SAAS,IACR,KAAK,EAAE,MAAM,EACb,UAAU,EAAC,gBAAgB,EAC3B,QAAQ,EAAE,KAAK,CAAC,EAAE;oBAChB,SAAS,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;gBAC/B,CAAC,GACD;YACF,oBAAC,gBAAgB,IACf,OAAO,EACL,oBAAC,QAAQ,IACP,OAAO,EAAE,CAAC,CAAC,SAAS,EACpB,QAAQ,EAAE,GAAG,EAAE,CAAC,YAAY,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,GACzC,EAEJ,KAAK,EAAC,iDAAiD,GACvD;YACF,oBAAC,aAAa;gBACZ,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,IAAI,EAAC,QAAQ,EACb,SAAS,QACT,QAAQ,EAAE,CAAC,EAAE,EACb,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,gBAAgB,CACpB,MAAM,KAAK,EAAE,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,SAAS,CAC9D,CAAA;wBACD,KAAK,CAAC,YAAY,CAAC,SAAS,CAAC,CAAA;wBAC7B,WAAW,EAAE,CAAA;oBACf,CAAC,aAGM;gBACT,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,WAAW,EACjB,OAAO,EAAE,GAAG,EAAE,CAAC,WAAW,EAAE,aAGrB,CACK,CACF,CACT,CACV,CAAA;AACH,CAAC;AAED,eAAe,QAAQ,CAAC,mBAAmB,CAAC,CAAA"}
1
+ {"version":3,"file":"SetFeatureHeight.js","sourceRoot":"","sources":["../../../src/LinearPileupDisplay/components/SetFeatureHeight.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AACvC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EACL,MAAM,EACN,QAAQ,EACR,aAAa,EACb,aAAa,EACb,gBAAgB,EAChB,SAAS,EACT,UAAU,GACX,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;AAEzC,SAAS,mBAAmB,CAAC,KAQ5B;IACC,MAAM,EAAE,KAAK,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IACpC,MAAM,EAAE,oBAAoB,EAAE,SAAS,EAAE,gBAAgB,EAAE,GAAG,KAAK,CAAA;IACnE,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,QAAQ,CAAC,GAAG,oBAAoB,EAAE,CAAC,CAAA;IAC/D,MAAM,CAAC,SAAS,EAAE,YAAY,CAAC,GAAG,QAAQ,CAAC,gBAAgB,CAAC,CAAA;IAE5D,MAAM,EAAE,GAAG,MAAM,KAAK,EAAE,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,MAAM,CAAC,CAAA;IAElD,OAAO,CACL,oBAAC,MAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW,EAAE,KAAK,EAAE,oBAAoB;QAC5D,oBAAC,aAAa;YACZ,oBAAC,UAAU,wKAIE;YACb,oBAAC,SAAS,IACR,KAAK,EAAE,MAAM,EACb,UAAU,EAAC,gBAAgB,EAC3B,QAAQ,EAAE,KAAK,CAAC,EAAE;oBAChB,SAAS,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;gBAC/B,CAAC,GACD;YACF,oBAAC,gBAAgB,IACf,OAAO,EACL,oBAAC,QAAQ,IACP,OAAO,EAAE,CAAC,CAAC,SAAS,EACpB,QAAQ,EAAE,GAAG,EAAE,CAAC,YAAY,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,GACzC,EAEJ,KAAK,EAAC,iDAAiD,GACvD;YACF,oBAAC,aAAa;gBACZ,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,IAAI,EAAC,QAAQ,EACb,SAAS,QACT,QAAQ,EAAE,CAAC,EAAE,EACb,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,gBAAgB,CACpB,MAAM,KAAK,EAAE,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,SAAS,CAC9D,CAAA;wBACD,KAAK,CAAC,YAAY,CAAC,SAAS,CAAC,CAAA;wBAC7B,WAAW,EAAE,CAAA;oBACf,CAAC,aAGM;gBACT,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,WAAW,EACjB,OAAO,EAAE,GAAG,EAAE,CAAC,WAAW,EAAE,aAGrB,CACK,CACF,CACT,CACV,CAAA;AACH,CAAC;AAED,eAAe,QAAQ,CAAC,mBAAmB,CAAC,CAAA"}
package/esm/LinearPileupDisplay/components/SetMaxHeight.js CHANGED
@@ -1,32 +1,19 @@
1
1
  import React, { useState } from 'react';
2
2
  import { observer } from 'mobx-react';
3
- import { Button, Dialog, DialogActions, DialogContent, DialogTitle, IconButton, TextField, Typography, } from '@mui/material';
3
+ import { Button, DialogActions, DialogContent, TextField, Typography, } from '@mui/material';
4
+ import { Dialog } from '@jbrowse/core/ui';
4
5
  import { makeStyles } from 'tss-react/mui';
5
- import CloseIcon from '@mui/icons-material/Close';
6
6
  const useStyles = makeStyles()(theme => ({
7
7
  root: {
8
8
  width: 500,
9
9
  },
10
- closeButton: {
11
- position: 'absolute',
12
- right: theme.spacing(1),
13
- top: theme.spacing(1),
14
- color: theme.palette.grey[500],
15
- },
16
- field: {
17
- margin: theme.spacing(2),
18
- },
19
10
  }));
20
11
  function SetMaxHeightDlg(props) {
21
12
  const { model, handleClose } = props;
22
13
  const { classes } = useStyles();
23
14
  const { maxHeight = '' } = model;
24
15
  const [max, setMax] = useState(`${maxHeight}`);
25
- return (React.createElement(Dialog, { open: true, onClose: handleClose },
26
- React.createElement(DialogTitle, null,
27
- "Filter options",
28
- React.createElement(IconButton, { "aria-label": "close", className: classes.closeButton, onClick: handleClose },
29
- React.createElement(CloseIcon, null))),
16
+ return (React.createElement(Dialog, { open: true, onClose: handleClose, title: "Filter options" },
30
17
  React.createElement(DialogContent, { className: classes.root },
31
18
  React.createElement(Typography, null, "Set max height for the track. For example, you can increase this if the layout says \"Max height reached\""),
32
19
  React.createElement(TextField, { value: max, onChange: event => {
package/esm/LinearPileupDisplay/components/SetMaxHeight.js.map CHANGED
@@ -1 +1 @@
1
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1
+ {"version":3,"file":"SetMaxHeight.js","sourceRoot":"","sources":["../../../src/LinearPileupDisplay/components/SetMaxHeight.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AACvC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EACL,MAAM,EACN,aAAa,EACb,aAAa,EACb,SAAS,EACT,UAAU,GACX,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;AACzC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,IAAI,EAAE;QACJ,KAAK,EAAE,GAAG;KACX;CACF,CAAC,CAAC,CAAA;AAEH,SAAS,eAAe,CAAC,KAMxB;IACC,MAAM,EAAE,KAAK,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IACpC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,SAAS,GAAG,EAAE,EAAE,GAAG,KAAK,CAAA;IAChC,MAAM,CAAC,GAAG,EAAE,MAAM,CAAC,GAAG,QAAQ,CAAC,GAAG,SAAS,EAAE,CAAC,CAAA;IAE9C,OAAO,CACL,oBAAC,MAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW,EAAE,KAAK,EAAC,gBAAgB;QACvD,oBAAC,aAAa,IAAC,SAAS,EAAE,OAAO,CAAC,IAAI;YACpC,oBAAC,UAAU,qHAGE;YACb,oBAAC,SAAS,IACR,KAAK,EAAE,GAAG,EACV,QAAQ,EAAE,KAAK,CAAC,EAAE;oBAChB,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;gBAC5B,CAAC,EACD,WAAW,EAAC,6BAA6B,GACzC;YACF,oBAAC,aAAa;gBACZ,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,IAAI,EAAC,QAAQ,EACb,SAAS,QACT,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,YAAY,CAChB,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;gBACT,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,WAAW,EACjB,OAAO,EAAE,GAAG,EAAE,CAAC,WAAW,EAAE,aAGrB,CACK,CACF,CACT,CACV,CAAA;AACH,CAAC;AAED,eAAe,QAAQ,CAAC,eAAe,CAAC,CAAA"}
package/esm/LinearPileupDisplay/components/SortByTag.js CHANGED
@@ -1,30 +1,12 @@
1
1
  import React, { useState } from 'react';
2
2
  import { observer } from 'mobx-react';
3
- import { Button, Dialog, DialogActions, DialogContent, DialogTitle, IconButton, TextField, Typography, } from '@mui/material';
4
- import { makeStyles } from 'tss-react/mui';
5
- import CloseIcon from '@mui/icons-material/Close';
6
- const useStyles = makeStyles()(theme => ({
7
- root: {
8
- margin: 0,
9
- padding: theme.spacing(2),
10
- },
11
- closeButton: {
12
- position: 'absolute',
13
- right: theme.spacing(1),
14
- top: theme.spacing(1),
15
- color: theme.palette.grey[500],
16
- },
17
- }));
3
+ import { Button, DialogActions, DialogContent, TextField, Typography, } from '@mui/material';
4
+ import { Dialog } from '@jbrowse/core/ui';
18
5
  function SortByTagDlg(props) {
19
- const { classes } = useStyles();
20
6
  const { model, handleClose } = props;
21
7
  const [tag, setTag] = useState('');
22
8
  const validTag = tag.match(/^[A-Za-z][A-Za-z0-9]$/);
23
- return (React.createElement(Dialog, { open: true, onClose: handleClose },
24
- React.createElement(DialogTitle, null,
25
- "Sort by tag",
26
- React.createElement(IconButton, { "aria-label": "close", className: classes.closeButton, onClick: handleClose },
27
- React.createElement(CloseIcon, null))),
9
+ return (React.createElement(Dialog, { open: true, onClose: handleClose, title: "Sort by tag" },
28
10
  React.createElement(DialogContent, null,
29
11
  React.createElement(Typography, null, "Set the tag to sort by"),
30
12
  React.createElement(Typography, { color: "textSecondary" }, "Examples: HP for haplotype, RG for read group, etc."),
package/esm/LinearPileupDisplay/components/SortByTag.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"SortByTag.js","sourceRoot":"","sources":["../../../src/LinearPileupDisplay/components/SortByTag.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AACvC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EACL,MAAM,EACN,MAAM,EACN,aAAa,EACb,aAAa,EACb,WAAW,EACX,UAAU,EACV,SAAS,EACT,UAAU,GACX,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,OAAO,SAAS,MAAM,2BAA2B,CAAA;AAEjD,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,IAAI,EAAE;QACJ,MAAM,EAAE,CAAC;QACT,OAAO,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;KAC1B;IACD,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,SAAS,YAAY,CAAC,KAGrB;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,KAAK,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IACpC,MAAM,CAAC,GAAG,EAAE,MAAM,CAAC,GAAG,QAAQ,CAAC,EAAE,CAAC,CAAA;IAClC,MAAM,QAAQ,GAAG,GAAG,CAAC,KAAK,CAAC,uBAAuB,CAAC,CAAA;IACnD,OAAO,CACL,oBAAC,MAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW;QAC/B,oBAAC,WAAW;;YAEV,oBAAC,UAAU,kBACE,OAAO,EAClB,SAAS,EAAE,OAAO,CAAC,WAAW,EAC9B,OAAO,EAAE,WAAW;gBAEpB,oBAAC,SAAS,OAAG,CACF,CACD;QACd,oBAAC,aAAa;YACZ,oBAAC,UAAU,iCAAoC;YAC/C,oBAAC,UAAU,IAAC,KAAK,EAAC,eAAe,0DAEpB;YACb,oBAAC,SAAS,IACR,KAAK,EAAE,GAAG,EACV,QAAQ,EAAE,KAAK,CAAC,EAAE,CAAC,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,EAC7C,WAAW,EAAC,gBAAgB,EAC5B,UAAU,EAAE;oBACV,SAAS,EAAE,CAAC;oBACZ,aAAa,EAAE,qBAAqB;iBACrC,EACD,KAAK,EAAE,GAAG,CAAC,MAAM,KAAK,CAAC,IAAI,CAAC,QAAQ,EACpC,UAAU,EAAE,GAAG,CAAC,MAAM,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAC,iBAAiB,CAAC,CAAC,CAAC,EAAE,EAClE,YAAY,EAAC,KAAK,iBACN,eAAe,GAC3B;YACF,oBAAC,aAAa;gBACZ,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,IAAI,EAAC,QAAQ,EACb,SAAS,QACT,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,WAAW,CAAC,KAAK,EAAE,GAAG,CAAC,CAAA;wBAC7B,WAAW,EAAE,CAAA;oBACf,CAAC,aAGM;gBACT,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,WAAW,EACjB,OAAO,EAAE,GAAG,EAAE,CAAC,WAAW,EAAE,aAGrB,CACK,CACF,CACT,CACV,CAAA;AACH,CAAC;AACD,eAAe,QAAQ,CAAC,YAAY,CAAC,CAAA"}
1
+ {"version":3,"file":"SortByTag.js","sourceRoot":"","sources":["../../../src/LinearPileupDisplay/components/SortByTag.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AACvC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EACL,MAAM,EACN,aAAa,EACb,aAAa,EACb,SAAS,EACT,UAAU,GACX,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;AAEzC,SAAS,YAAY,CAAC,KAGrB;IACC,MAAM,EAAE,KAAK,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IACpC,MAAM,CAAC,GAAG,EAAE,MAAM,CAAC,GAAG,QAAQ,CAAC,EAAE,CAAC,CAAA;IAClC,MAAM,QAAQ,GAAG,GAAG,CAAC,KAAK,CAAC,uBAAuB,CAAC,CAAA;IACnD,OAAO,CACL,oBAAC,MAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW,EAAE,KAAK,EAAC,aAAa;QACpD,oBAAC,aAAa;YACZ,oBAAC,UAAU,iCAAoC;YAC/C,oBAAC,UAAU,IAAC,KAAK,EAAC,eAAe,0DAEpB;YACb,oBAAC,SAAS,IACR,KAAK,EAAE,GAAG,EACV,QAAQ,EAAE,KAAK,CAAC,EAAE,CAAC,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,EAC7C,WAAW,EAAC,gBAAgB,EAC5B,UAAU,EAAE;oBACV,SAAS,EAAE,CAAC;oBACZ,aAAa,EAAE,qBAAqB;iBACrC,EACD,KAAK,EAAE,GAAG,CAAC,MAAM,KAAK,CAAC,IAAI,CAAC,QAAQ,EACpC,UAAU,EAAE,GAAG,CAAC,MAAM,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAC,iBAAiB,CAAC,CAAC,CAAC,EAAE,EAClE,YAAY,EAAC,KAAK,iBACN,eAAe,GAC3B;YACF,oBAAC,aAAa;gBACZ,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,IAAI,EAAC,QAAQ,EACb,SAAS,QACT,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,WAAW,CAAC,KAAK,EAAE,GAAG,CAAC,CAAA;wBAC7B,WAAW,EAAE,CAAA;oBACf,CAAC,aAGM;gBACT,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,WAAW,EACjB,OAAO,EAAE,GAAG,EAAE,CAAC,WAAW,EAAE,aAGrB,CACK,CACF,CACT,CACV,CAAA;AACH,CAAC;AACD,eAAe,QAAQ,CAAC,YAAY,CAAC,CAAA"}
package/esm/LinearPileupDisplay/configSchema.d.ts CHANGED
@@ -1,6 +1,6 @@
1
1
  import { Instance } from 'mobx-state-tree';
2
2
  import PluginManager from '@jbrowse/core/PluginManager';
3
- declare function PileupConfigFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
4
- export declare type LinearPileupDisplayConfigModel = ReturnType<typeof PileupConfigFactory>;
5
- export declare type LinearPileupDisplayConfig = Instance<LinearPileupDisplayConfigModel>;
6
- export default PileupConfigFactory;
3
+ declare function configSchemaF(pluginManager: PluginManager): import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
4
+ export type LinearPileupDisplayConfigModel = ReturnType<typeof configSchemaF>;
5
+ export type LinearPileupDisplayConfig = Instance<LinearPileupDisplayConfigModel>;
6
+ export default configSchemaF;
package/esm/LinearPileupDisplay/configSchema.js CHANGED
@@ -5,7 +5,7 @@ import { types } from 'mobx-state-tree';
5
5
  * #config LinearPileupDisplay
6
6
  */
7
7
  function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
8
- function PileupConfigFactory(pluginManager) {
8
+ function configSchemaF(pluginManager) {
9
9
  // modify config schema to take in a sub coverage display
10
10
  return ConfigurationSchema('LinearPileupDisplay', {
11
11
  /**
@@ -54,5 +54,5 @@ function PileupConfigFactory(pluginManager) {
54
54
  explicitlyTyped: true,
55
55
  });
56
56
  }
57
- export default PileupConfigFactory;
57
+ export default configSchemaF;
58
58
  //# sourceMappingURL=configSchema.js.map
package/esm/LinearPileupDisplay/configSchema.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/LinearPileupDisplay/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE,OAAO,EAAE,qCAAqC,EAAE,MAAM,oCAAoC,CAAA;AAC1F,OAAO,EAAE,KAAK,EAAY,MAAM,iBAAiB,CAAA;AAGjD;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,SAAS,mBAAmB,CAAC,aAA4B;IACvD,yDAAyD;IACzD,OAAO,mBAAmB,CACxB,qBAAqB,EACrB;QACE;;WAEG;QACH,gBAAgB,EAAE;YAChB,IAAI,EAAE,YAAY;YAClB,KAAK,EAAE,KAAK,CAAC,WAAW,CAAC,WAAW,EAAE,CAAC,QAAQ,CAAC,CAAC;YACjD,YAAY,EAAE,QAAQ;SACvB;QACD;;WAEG;QACH,SAAS,EAAE,mBAAmB,CAAC,wBAAwB,EAAE;YACvD,cAAc,EACZ,aAAa,CAAC,eAAe,CAAC,gBAAgB,CAAC,CAAC,YAAY;SAC/D,CAAC;QACF;;WAEG;QACH,uBAAuB,EAAE;YACvB,IAAI,EAAE,QAAQ;YACd,WAAW,EAAE,0DAA0D;YACvE,YAAY,EAAE,CAAC;SAChB;QAED;;WAEG;QACH,WAAW,EAAE;YACX,IAAI,EAAE,YAAY;YAClB,KAAK,EAAE,KAAK,CAAC,WAAW,CAAC,aAAa,EAAE;gBACtC,QAAQ;gBACR,QAAQ;gBACR,YAAY;gBACZ,0BAA0B;gBAC1B,gBAAgB;gBAChB,KAAK;aACN,CAAC;YACF,WAAW,EAAE,qBAAqB;YAClC,YAAY,EAAE,QAAQ;SACvB;KACF,EACD;QACE;;WAEG;QACH,iBAAiB,EAAE,qCAAqC,CAAC,aAAa,CAAC;QACvE,eAAe,EAAE,IAAI;KACtB,CACF,CAAA;AACH,CAAC;AAMD,eAAe,mBAAmB,CAAA"}
1
+ {"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/LinearPileupDisplay/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE,OAAO,EAAE,qCAAqC,EAAE,MAAM,oCAAoC,CAAA;AAC1F,OAAO,EAAE,KAAK,EAAY,MAAM,iBAAiB,CAAA;AAGjD;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,SAAS,aAAa,CAAC,aAA4B;IACjD,yDAAyD;IACzD,OAAO,mBAAmB,CACxB,qBAAqB,EACrB;QACE;;WAEG;QACH,gBAAgB,EAAE;YAChB,IAAI,EAAE,YAAY;YAClB,KAAK,EAAE,KAAK,CAAC,WAAW,CAAC,WAAW,EAAE,CAAC,QAAQ,CAAC,CAAC;YACjD,YAAY,EAAE,QAAQ;SACvB;QACD;;WAEG;QACH,SAAS,EAAE,mBAAmB,CAAC,wBAAwB,EAAE;YACvD,cAAc,EACZ,aAAa,CAAC,eAAe,CAAC,gBAAgB,CAAC,CAAC,YAAY;SAC/D,CAAC;QACF;;WAEG;QACH,uBAAuB,EAAE;YACvB,IAAI,EAAE,QAAQ;YACd,WAAW,EAAE,0DAA0D;YACvE,YAAY,EAAE,CAAC;SAChB;QAED;;WAEG;QACH,WAAW,EAAE;YACX,IAAI,EAAE,YAAY;YAClB,KAAK,EAAE,KAAK,CAAC,WAAW,CAAC,aAAa,EAAE;gBACtC,QAAQ;gBACR,QAAQ;gBACR,YAAY;gBACZ,0BAA0B;gBAC1B,gBAAgB;gBAChB,KAAK;aACN,CAAC;YACF,WAAW,EAAE,qBAAqB;YAClC,YAAY,EAAE,QAAQ;SACvB;KACF,EACD;QACE;;WAEG;QACH,iBAAiB,EAAE,qCAAqC,CAAC,aAAa,CAAC;QACvE,eAAe,EAAE,IAAI;KACtB,CACF,CAAA;AACH,CAAC;AAID,eAAe,aAAa,CAAA"}
package/esm/LinearPileupDisplay/index.d.ts CHANGED
@@ -1,2 +1,5 @@
1
+ import configSchemaFactory from './configSchema';
2
+ import modelFactory from './model';
1
3
  import PluginManager from '@jbrowse/core/PluginManager';
2
4
  export default function register(pluginManager: PluginManager): void;
5
+ export { modelFactory as linearPileupDisplayStateModelFactory, configSchemaFactory as linearPileupDisplayConfigSchemaFactory, };
package/esm/LinearPileupDisplay/index.js CHANGED
@@ -15,4 +15,5 @@ export default function register(pluginManager) {
15
15
  });
16
16
  });
17
17
  }
18
+ export { modelFactory as linearPileupDisplayStateModelFactory, configSchemaFactory as linearPileupDisplayConfigSchemaFactory, };
18
19
  //# sourceMappingURL=index.js.map
package/esm/LinearPileupDisplay/index.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearPileupDisplay/index.ts"],"names":[],"mappings":"AAAA,OAAO,mBAAmB,MAAM,gBAAgB,CAAA;AAChD,OAAO,YAAY,MAAM,SAAS,CAAA;AAClC,OAAO,WAAW,MAAM,iDAAiD,CAAA;AAEzE,OAAO,EAAE,0BAA0B,EAAE,MAAM,oCAAoC,CAAA;AAE/E,MAAM,CAAC,OAAO,UAAU,QAAQ,CAAC,aAA4B;IAC3D,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,YAAY,GAAG,mBAAmB,CAAC,aAAa,CAAC,CAAA;QACvD,OAAO,IAAI,WAAW,CAAC;YACrB,IAAI,EAAE,qBAAqB;YAC3B,YAAY;YACZ,UAAU,EAAE,YAAY,CAAC,YAAY,CAAC;YACtC,SAAS,EAAE,iBAAiB;YAC5B,QAAQ,EAAE,kBAAkB;YAC5B,cAAc,EAAE,0BAA0B;SAC3C,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC"}
1
+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearPileupDisplay/index.ts"],"names":[],"mappings":"AAAA,OAAO,mBAAmB,MAAM,gBAAgB,CAAA;AAChD,OAAO,YAAY,MAAM,SAAS,CAAA;AAClC,OAAO,WAAW,MAAM,iDAAiD,CAAA;AAEzE,OAAO,EAAE,0BAA0B,EAAE,MAAM,oCAAoC,CAAA;AAE/E,MAAM,CAAC,OAAO,UAAU,QAAQ,CAAC,aAA4B;IAC3D,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,YAAY,GAAG,mBAAmB,CAAC,aAAa,CAAC,CAAA;QACvD,OAAO,IAAI,WAAW,CAAC;YACrB,IAAI,EAAE,qBAAqB;YAC3B,YAAY;YACZ,UAAU,EAAE,YAAY,CAAC,YAAY,CAAC;YACtC,SAAS,EAAE,iBAAiB;YAC5B,QAAQ,EAAE,kBAAkB;YAC5B,cAAc,EAAE,0BAA0B;SAC3C,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC;AAED,OAAO,EACL,YAAY,IAAI,oCAAoC,EACpD,mBAAmB,IAAI,sCAAsC,GAC9D,CAAA"}
package/esm/LinearPileupDisplay/model.d.ts CHANGED
@@ -6,6 +6,7 @@ import { ContentCopy as ContentCopyIcon } from '@jbrowse/core/ui/Icons';
6
6
  import { LinearPileupDisplayConfigModel } from './configSchema';
7
7
  /**
8
8
  * #stateModel LinearPileupDisplay
9
+ * extends `BaseLinearDisplay`
9
10
  */
10
11
  declare function stateModelFactory(configSchema: LinearPileupDisplayConfigModel): import("mobx-state-tree").IModelType<{
11
12
  id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
@@ -29,10 +30,14 @@ declare function stateModelFactory(configSchema: LinearPileupDisplayConfigModel)
29
30
  isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
30
31
  isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
31
32
  }, {
32
- renderInProgress: AbortController | undefined;
33
+ renderInProgress: AbortController | undefined; /**
34
+ * #property
35
+ */
33
36
  filled: boolean;
34
37
  reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
35
- features: Map<string, Feature> | undefined;
38
+ features: Map<string, Feature> | undefined; /**
39
+ * #property
40
+ */
36
41
  layout: any;
37
42
  status: string;
38
43
  error: unknown;
@@ -43,7 +48,9 @@ declare function stateModelFactory(configSchema: LinearPileupDisplayConfigModel)
43
48
  }) => any;
44
49
  renderProps: any;
45
50
  } & {
46
- doReload(): void;
51
+ doReload(): void; /**
52
+ * #property
53
+ */
47
54
  afterAttach(): void;
48
55
  setStatus(message: string): void;
49
56
  setLoading(abortController: AbortController): void;
@@ -104,9 +111,7 @@ declare function stateModelFactory(configSchema: LinearPileupDisplayConfigModel)
104
111
  rendererTypeName: string;
105
112
  error: unknown;
106
113
  } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
107
- id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>; /**
108
- * #action
109
- */
114
+ id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
110
115
  type: import("mobx-state-tree").ISimpleType<string>;
111
116
  rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
112
117
  }, {
@@ -221,12 +226,17 @@ declare function stateModelFactory(configSchema: LinearPileupDisplayConfigModel)
221
226
  colorTagMap: import("mobx").ObservableMap<string, string>;
222
227
  modificationTagMap: import("mobx").ObservableMap<string, string>;
223
228
  featureUnderMouseVolatile: Feature | undefined;
229
+ currSortBpPerPx: number;
224
230
  ready: boolean;
225
231
  } & {
226
232
  /**
227
233
  * #action
228
234
  */
229
235
  setReady(flag: boolean): void;
236
+ /**
237
+ * #action
238
+ */
239
+ setCurrSortBpPerPx(n: number): void;
230
240
  /**
231
241
  * #action
232
242
  */
@@ -409,12 +419,12 @@ declare function stateModelFactory(configSchema: LinearPileupDisplayConfigModel)
409
419
  })[];
410
420
  }, import("mobx-state-tree")._NotCustomized, {
411
421
  type: string;
412
- id: string;
413
422
  height: number;
423
+ id: string;
414
424
  rpcDriverName: string | undefined;
415
425
  userBpPerPxLimit: number | undefined;
416
426
  userByteSizeLimit: number | undefined;
417
427
  } & import("mobx-state-tree")._NotCustomized>;
418
- export declare type LinearPileupDisplayStateModel = ReturnType<typeof stateModelFactory>;
419
- export declare type LinearPileupDisplayModel = Instance<LinearPileupDisplayStateModel>;
428
+ export type LinearPileupDisplayStateModel = ReturnType<typeof stateModelFactory>;
429
+ export type LinearPileupDisplayModel = Instance<LinearPileupDisplayStateModel>;
420
430
  export default stateModelFactory;
package/esm/LinearPileupDisplay/model.js CHANGED
@@ -29,6 +29,7 @@ const rendererTypes = new Map([
29
29
  ]);
30
30
  /**
31
31
  * #stateModel LinearPileupDisplay
32
+ * extends `BaseLinearDisplay`
32
33
  */
33
34
  function stateModelFactory(configSchema) {
34
35
  return types
@@ -83,6 +84,9 @@ function stateModelFactory(configSchema) {
83
84
  tag: types.maybe(types.string),
84
85
  extra: types.frozen(),
85
86
  })),
87
+ /**
88
+ * #property
89
+ */
86
90
  filterBy: types.optional(types.model({
87
91
  flagInclude: types.optional(types.number, 0),
88
92
  flagExclude: types.optional(types.number, 1540),
@@ -94,6 +98,7 @@ function stateModelFactory(configSchema) {
94
98
  colorTagMap: observable.map({}),
95
99
  modificationTagMap: observable.map({}),
96
100
  featureUnderMouseVolatile: undefined,
101
+ currSortBpPerPx: 0,
97
102
  ready: false,
98
103
  }))
99
104
  .actions(self => ({
@@ -103,6 +108,12 @@ function stateModelFactory(configSchema) {
103
108
  setReady(flag) {
104
109
  self.ready = flag;
105
110
  },
111
+ /**
112
+ * #action
113
+ */
114
+ setCurrSortBpPerPx(n) {
115
+ self.currSortBpPerPx = n;
116
+ },
106
117
  /**
107
118
  * #action
108
119
  */
@@ -220,7 +231,7 @@ function stateModelFactory(configSchema) {
220
231
  ...self.renderProps(),
221
232
  });
222
233
  self.setReady(true);
223
- self.setCurrBpPerPx(bpPerPx);
234
+ self.setCurrSortBpPerPx(bpPerPx);
224
235
  }
225
236
  else {
226
237
  self.setReady(true);
@@ -232,6 +243,8 @@ function stateModelFactory(configSchema) {
232
243
  }
233
244
  }, { delay: 1000 }));
234
245
  // autorun synchronizes featureUnderMouse with featureIdUnderMouse
246
+ // asynchronously. this is needed due to how we do not serialize all
247
+ // features from the BAM/CRAM over the rpc
235
248
  addDisposer(self, autorun(async () => {
236
249
  var _a;
237
250
  const session = getSession(self);
@@ -451,13 +464,13 @@ function stateModelFactory(configSchema) {
451
464
  */
452
465
  renderProps() {
453
466
  const view = getContainingView(self);
454
- const { colorTagMap, modificationTagMap, sortedBy, colorBy, filterBy, rpcDriverName, currBpPerPx, ready, } = self;
467
+ const { colorTagMap, modificationTagMap, sortedBy, colorBy, filterBy, rpcDriverName, currSortBpPerPx, ready, } = self;
455
468
  const superProps = superRenderProps();
456
469
  return {
457
470
  ...superProps,
458
471
  notReady: superProps.notReady ||
459
472
  !ready ||
460
- (sortedBy && currBpPerPx !== view.bpPerPx),
473
+ (sortedBy && currSortBpPerPx !== view.bpPerPx),
461
474
  rpcDriverName,
462
475
  displayModel: self,
463
476
  sortedBy,
@@ -576,39 +589,27 @@ function stateModelFactory(configSchema) {
576
589
  subMenu: [
577
590
  {
578
591
  label: 'Normal',
579
- onClick: () => {
580
- self.setColorScheme({ type: 'normal' });
581
- },
592
+ onClick: () => self.setColorScheme({ type: 'normal' }),
582
593
  },
583
594
  {
584
595
  label: 'Mapping quality',
585
- onClick: () => {
586
- self.setColorScheme({ type: 'mappingQuality' });
587
- },
596
+ onClick: () => self.setColorScheme({ type: 'mappingQuality' }),
588
597
  },
589
598
  {
590
599
  label: 'Strand',
591
- onClick: () => {
592
- self.setColorScheme({ type: 'strand' });
593
- },
600
+ onClick: () => self.setColorScheme({ type: 'strand' }),
594
601
  },
595
602
  {
596
603
  label: 'Pair orientation',
597
- onClick: () => {
598
- self.setColorScheme({ type: 'pairOrientation' });
599
- },
604
+ onClick: () => self.setColorScheme({ type: 'pairOrientation' }),
600
605
  },
601
606
  {
602
607
  label: 'Per-base quality',
603
- onClick: () => {
604
- self.setColorScheme({ type: 'perBaseQuality' });
605
- },
608
+ onClick: () => self.setColorScheme({ type: 'perBaseQuality' }),
606
609
  },
607
610
  {
608
611
  label: 'Per-base lettering',
609
- onClick: () => {
610
- self.setColorScheme({ type: 'perBaseLettering' });
611
- },
612
+ onClick: () => self.setColorScheme({ type: 'perBaseLettering' }),
612
613
  },
613
614
  {
614
615
  label: 'Modifications or methylation',
@@ -621,15 +622,11 @@ function stateModelFactory(configSchema) {
621
622
  },
622
623
  {
623
624
  label: 'Insert size',
624
- onClick: () => {
625
- self.setColorScheme({ type: 'insertSize' });
626
- },
625
+ onClick: () => self.setColorScheme({ type: 'insertSize' }),
627
626
  },
628
627
  {
629
628
  label: 'Stranded paired-end',
630
- onClick: () => {
631
- self.setColorScheme({ type: 'reverseTemplate' });
632
- },
629
+ onClick: () => self.setColorScheme({ type: 'reverseTemplate' }),
633
630
  },
634
631
  {
635
632
  label: 'Color by tag...',
@@ -674,9 +671,7 @@ function stateModelFactory(configSchema) {
674
671
  label: 'Fade mismatches by quality',
675
672
  type: 'checkbox',
676
673
  checked: self.mismatchAlphaSetting,
677
- onClick: () => {
678
- self.toggleMismatchAlpha();
679
- },
674
+ onClick: () => self.toggleMismatchAlpha(),
680
675
  },
681
676
  ];
682
677
  },
package/esm/LinearPileupDisplay/model.js.map CHANGED
@@ -1 +1 @@
1
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1
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package/esm/LinearSNPCoverageDisplay/components/Tooltip.d.ts CHANGED
@@ -1,6 +1,6 @@
1
1
  /// <reference types="react" />
2
2
  import { Feature } from '@jbrowse/core/util/simpleFeature';
3
- declare type Coord = [number, number];
3
+ type Coord = [number, number];
4
4
  declare const SNPCoverageTooltip: (props: {
5
5
  model: {
6
6
  featureUnderMouse: Feature;