react-msaview 3.0.0 → 3.0.2

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Files changed (84) hide show
  1. package/bundle/index.js +31 -31
  2. package/dist/components/Header.js +4 -9
  3. package/dist/components/Header.js.map +1 -1
  4. package/dist/components/HeaderInfoArea.d.ts +6 -0
  5. package/dist/components/HeaderInfoArea.js +12 -0
  6. package/dist/components/HeaderInfoArea.js.map +1 -0
  7. package/dist/components/MSAPanel/Loading.d.ts +2 -0
  8. package/dist/components/MSAPanel/Loading.js +12 -0
  9. package/dist/components/MSAPanel/Loading.js.map +1 -0
  10. package/dist/components/MSAPanel/MSACanvas.js +1 -10
  11. package/dist/components/MSAPanel/MSACanvas.js.map +1 -1
  12. package/dist/components/MSAPanel/MSAMouseoverCanvas.js +1 -22
  13. package/dist/components/MSAPanel/MSAMouseoverCanvas.js.map +1 -1
  14. package/dist/components/MSAPanel/renderMSABlock.js +0 -1
  15. package/dist/components/MSAPanel/renderMSABlock.js.map +1 -1
  16. package/dist/components/MSAPanel/renderMSAMouseover.d.ts +5 -0
  17. package/dist/components/MSAPanel/renderMSAMouseover.js +24 -0
  18. package/dist/components/MSAPanel/renderMSAMouseover.js.map +1 -0
  19. package/dist/components/Minimap.js +13 -13
  20. package/dist/components/Minimap.js.map +1 -1
  21. package/dist/components/TreePanel/TreeCanvasBlock.js +8 -4
  22. package/dist/components/TreePanel/TreeCanvasBlock.js.map +1 -1
  23. package/dist/components/TreePanel/{TreeMenu.d.ts → TreeNodeMenu.d.ts} +1 -0
  24. package/dist/components/TreePanel/{TreeMenu.js → TreeNodeMenu.js} +8 -4
  25. package/dist/components/TreePanel/TreeNodeMenu.js.map +1 -0
  26. package/dist/components/TreePanel/dialogs/{TreeNodeInfoDlg.js → TreeNodeInfoDialog.js} +2 -2
  27. package/dist/components/TreePanel/dialogs/TreeNodeInfoDialog.js.map +1 -0
  28. package/dist/components/TreePanel/renderTreeCanvas.d.ts +8 -3
  29. package/dist/components/TreePanel/renderTreeCanvas.js +8 -7
  30. package/dist/components/TreePanel/renderTreeCanvas.js.map +1 -1
  31. package/dist/components/dialogs/SettingsDialog.js +31 -22
  32. package/dist/components/dialogs/SettingsDialog.js.map +1 -1
  33. package/dist/model.d.ts +120 -62
  34. package/dist/model.js +176 -124
  35. package/dist/model.js.map +1 -1
  36. package/dist/parsers/ClustalMSA.d.ts +18 -5
  37. package/dist/parsers/ClustalMSA.js +1 -1
  38. package/dist/parsers/ClustalMSA.js.map +1 -1
  39. package/dist/parsers/FastaMSA.d.ts +1 -1
  40. package/dist/parsers/FastaMSA.js +2 -2
  41. package/dist/parsers/FastaMSA.js.map +1 -1
  42. package/dist/parsers/StockholmMSA.d.ts +1 -1
  43. package/dist/parsers/StockholmMSA.js +2 -2
  44. package/dist/parsers/StockholmMSA.js.map +1 -1
  45. package/dist/util.d.ts +1 -0
  46. package/dist/util.js +15 -7
  47. package/dist/util.js.map +1 -1
  48. package/dist/version.d.ts +1 -1
  49. package/dist/version.js +1 -1
  50. package/package.json +9 -7
  51. package/src/components/Header.tsx +5 -11
  52. package/src/components/HeaderInfoArea.tsx +21 -0
  53. package/src/components/MSAPanel/Loading.tsx +16 -0
  54. package/src/components/MSAPanel/MSACanvas.tsx +1 -16
  55. package/src/components/MSAPanel/MSAMouseoverCanvas.tsx +2 -50
  56. package/src/components/MSAPanel/renderMSABlock.ts +0 -2
  57. package/src/components/MSAPanel/renderMSAMouseover.ts +51 -0
  58. package/src/components/Minimap.tsx +15 -15
  59. package/src/components/TreePanel/TreeCanvasBlock.tsx +8 -3
  60. package/src/components/TreePanel/{TreeMenu.tsx → TreeNodeMenu.tsx} +12 -3
  61. package/src/components/TreePanel/dialogs/{TreeNodeInfoDlg.tsx → TreeNodeInfoDialog.tsx} +1 -1
  62. package/src/components/TreePanel/renderTreeCanvas.ts +13 -4
  63. package/src/components/dialogs/SettingsDialog.tsx +61 -44
  64. package/src/model.ts +279 -154
  65. package/src/parsers/ClustalMSA.ts +1 -1
  66. package/src/parsers/FastaMSA.ts +1 -1
  67. package/src/parsers/StockholmMSA.ts +1 -1
  68. package/src/util.ts +19 -6
  69. package/src/version.ts +1 -1
  70. package/dist/components/OverviewRubberband.d.ts +0 -8
  71. package/dist/components/OverviewRubberband.js +0 -185
  72. package/dist/components/OverviewRubberband.js.map +0 -1
  73. package/dist/components/Rubberband.d.ts +0 -8
  74. package/dist/components/Rubberband.js +0 -185
  75. package/dist/components/Rubberband.js.map +0 -1
  76. package/dist/components/TreePanel/TreeMenu.js.map +0 -1
  77. package/dist/components/TreePanel/dialogs/TreeNodeInfoDlg.js.map +0 -1
  78. package/dist/components/dialogs/AnnotationDialog.d.ts +0 -11
  79. package/dist/components/dialogs/AnnotationDialog.js +0 -65
  80. package/dist/components/dialogs/AnnotationDialog.js.map +0 -1
  81. package/src/components/OverviewRubberband.tsx +0 -283
  82. package/src/components/Rubberband.tsx +0 -283
  83. package/src/components/dialogs/AnnotationDialog.tsx +0 -144
  84. /package/dist/components/TreePanel/dialogs/{TreeNodeInfoDlg.d.ts → TreeNodeInfoDialog.d.ts} +0 -0
@@ -8,47 +8,56 @@ const useStyles = makeStyles()(theme => ({
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  field: {
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  margin: theme.spacing(4),
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  },
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+ flex: {
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+ display: 'flex',
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+ },
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  }));
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- const SettingsDialog = observer(function ({ model, onClose, }) {
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+ function FormControlLabel2(rest) {
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+ return (React.createElement("div", null,
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+ React.createElement(FormControlLabel, { ...rest })));
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+ }
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+ const SettingsContent = observer(function ({ model }) {
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  const { classes } = useStyles();
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  const { bgColor, colWidth, colorSchemeName, drawTree, drawNodeBubbles, labelsAlignRight, noTree, rowHeight, showBranchLen, treeWidthMatchesArea, treeWidth, } = model;
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- return (React.createElement(Dialog, { open: true, onClose: () => onClose(), title: "Settings" },
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- React.createElement(DialogContent, null,
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- React.createElement(FormControlLabel, { control: React.createElement(Checkbox, { checked: showBranchLen, onChange: () => model.setShowBranchLen(!showBranchLen) }), label: "Show branch length" }),
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- React.createElement(FormControlLabel, { control: React.createElement(Checkbox, { checked: bgColor, onChange: () => model.setBgColor(!bgColor) }), label: "Color background" }),
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- React.createElement(FormControlLabel, { control: React.createElement(Checkbox, { checked: drawNodeBubbles, onChange: () => model.setDrawNodeBubbles(!drawNodeBubbles) }), label: "Draw node bubbles" }),
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- React.createElement(FormControlLabel, { control: React.createElement(Checkbox, { checked: drawTree, onChange: () => model.setDrawTree(!drawTree) }), label: "Draw tree (if available)" }),
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- React.createElement(FormControlLabel, { control: React.createElement(Checkbox, { checked: labelsAlignRight, onChange: () => model.setLabelsAlignRight(!labelsAlignRight) }), label: "Labels align right" }),
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+ return (React.createElement(React.Fragment, null,
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+ React.createElement("div", null,
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+ React.createElement(Button, { onClick: () => model.clearHidden() }, "Clear hidden"),
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+ React.createElement("h1", null, "Tree options"),
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+ React.createElement(FormControlLabel2, { control: React.createElement(Checkbox, { checked: showBranchLen, onChange: () => model.setShowBranchLen(!showBranchLen) }), label: "Show branch length?" }),
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+ React.createElement(FormControlLabel2, { control: React.createElement(Checkbox, { checked: drawNodeBubbles, onChange: () => model.setDrawNodeBubbles(!drawNodeBubbles) }), label: "Draw clickable bubbles on tree branches?" }),
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+ React.createElement(FormControlLabel2, { control: React.createElement(Checkbox, { checked: drawTree, onChange: () => model.setDrawTree(!drawTree) }), label: "Show tree?" }),
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+ React.createElement(FormControlLabel2, { control: React.createElement(Checkbox, { checked: labelsAlignRight, onChange: () => model.setLabelsAlignRight(!labelsAlignRight) }), label: "Tree labels align right?" }),
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  !noTree ? (React.createElement("div", null,
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- React.createElement(FormControlLabel, { control: React.createElement(Checkbox, { checked: treeWidthMatchesArea, onChange: () => model.setTreeWidthMatchesArea(!treeWidthMatchesArea) }), label: "Make tree width fit to tree area?" }),
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- !treeWidthMatchesArea ? (React.createElement("div", { style: { display: 'flex' } },
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+ React.createElement(FormControlLabel2, { control: React.createElement(Checkbox, { checked: treeWidthMatchesArea, onChange: () => model.setTreeWidthMatchesArea(!treeWidthMatchesArea) }), label: "Make tree width fit to tree area?" }),
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+ !treeWidthMatchesArea ? (React.createElement("div", { className: classes.flex },
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  React.createElement(Typography, null,
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  "Tree width (",
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  treeWidth,
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  "px)"),
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- React.createElement(Slider, { className: classes.field, min: 50, max: 600, value: treeWidth, onChange: (_, val) => model.setTreeWidth(val) }))) : null)) : null,
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- React.createElement("div", { style: { display: 'flex' } },
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+ React.createElement(Slider, { className: classes.field, min: 50, max: 600, value: treeWidth, onChange: (_, val) => model.setTreeWidth(val) }))) : null)) : null),
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+ React.createElement("div", null,
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+ React.createElement("h1", null, "MSA options"),
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+ React.createElement(FormControlLabel2, { control: React.createElement(Checkbox, { checked: bgColor, onChange: () => model.setBgColor(!bgColor) }), label: "Color background tiles of MSA?" }),
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+ React.createElement("div", { className: classes.flex },
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  React.createElement(Typography, null,
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  "Column width (",
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  colWidth,
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  "px)"),
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  React.createElement(Slider, { className: classes.field, min: 1, max: 50, value: colWidth, onChange: (_, val) => model.setColWidth(val) })),
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- React.createElement("div", { style: { display: 'flex' } },
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+ React.createElement("div", { className: classes.flex },
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  React.createElement(Typography, null,
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  "Row height (",
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  rowHeight,
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  "px)"),
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  React.createElement(Slider, { className: classes.field, min: 1, max: 50, value: rowHeight, onChange: (_, val) => model.setRowHeight(val) })),
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- React.createElement(TextField, { select: true, label: "Color scheme", value: colorSchemeName, onChange: event => model.setColorSchemeName(event.target.value) }, Object.keys(colorSchemes).map(option => (React.createElement(MenuItem, { key: option, value: option }, option)))),
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+ React.createElement(TextField, { select: true, label: "Color scheme", value: colorSchemeName, onChange: event => model.setColorSchemeName(event.target.value) }, Object.keys(colorSchemes).map(option => (React.createElement(MenuItem, { key: option, value: option }, option)))))));
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+ });
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+ const SettingsDialog = observer(function ({ model, onClose, }) {
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+ return (React.createElement(Dialog, { open: true, onClose: () => onClose(), title: "Settings" },
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+ React.createElement(DialogContent, null,
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+ React.createElement(SettingsContent, { model: model }),
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  React.createElement(DialogActions, null,
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- React.createElement(Button, { onClick: () => {
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- model.setRowHeight(+rowHeight);
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- model.setColWidth(+colWidth);
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- if (!noTree) {
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- model.setTreeWidth(+treeWidth);
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- }
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- onClose();
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- }, variant: "contained", color: "primary" }, "Submit")))));
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+ React.createElement(Button, { onClick: () => onClose(), variant: "contained", color: "primary" }, "Submit")))));
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  });
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  export default SettingsDialog;
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  //# sourceMappingURL=SettingsDialog.js.map
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1
+ {"version":3,"file":"SettingsDialog.js","sourceRoot":"","sources":["../../../src/components/dialogs/SettingsDialog.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;AACzC,OAAO,EACL,MAAM,EACN,QAAQ,EACR,aAAa,EACb,aAAa,EACb,gBAAgB,EAEhB,QAAQ,EACR,MAAM,EACN,SAAS,EACT,UAAU,GACX,MAAM,eAAe,CAAA;AAGtB,OAAO,YAAY,MAAM,oBAAoB,CAAA;AAE7C,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,KAAK,EAAE;QACL,MAAM,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;KACzB;IACD,IAAI,EAAE;QACJ,OAAO,EAAE,MAAM;KAChB;CACF,CAAC,CAAC,CAAA;AAEH,SAAS,iBAAiB,CAAC,IAA2B;IACpD,OAAO,CACL;QACE,oBAAC,gBAAgB,OAAK,IAAI,GAAI,CAC1B,CACP,CAAA;AACH,CAAC;AAED,MAAM,eAAe,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IAC3E,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EACJ,OAAO,EACP,QAAQ,EACR,eAAe,EACf,QAAQ,EACR,eAAe,EACf,gBAAgB,EAChB,MAAM,EACN,SAAS,EACT,aAAa,EACb,oBAAoB,EACpB,SAAS,GACV,GAAG,KAAK,CAAA;IACT,OAAO,CACL;QACE;YACE,oBAAC,MAAM,IAAC,OAAO,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,WAAW,EAAE,mBAAuB;YACjE,+CAAqB;YACrB,oBAAC,iBAAiB,IAChB,OAAO,EACL,oBAAC,QAAQ,IACP,OAAO,EAAE,aAAa,EACtB,QAAQ,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,gBAAgB,CAAC,CAAC,aAAa,CAAC,GACtD,EAEJ,KAAK,EAAC,qBAAqB,GAC3B;YAEF,oBAAC,iBAAiB,IAChB,OAAO,EACL,oBAAC,QAAQ,IACP,OAAO,EAAE,eAAe,EACxB,QAAQ,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,kBAAkB,CAAC,CAAC,eAAe,CAAC,GAC1D,EAEJ,KAAK,EAAC,0CAA0C,GAChD;YACF,oBAAC,iBAAiB,IAChB,OAAO,EACL,oBAAC,QAAQ,IACP,OAAO,EAAE,QAAQ,EACjB,QAAQ,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,WAAW,CAAC,CAAC,QAAQ,CAAC,GAC5C,EAEJ,KAAK,EAAC,YAAY,GAClB;YAEF,oBAAC,iBAAiB,IAChB,OAAO,EACL,oBAAC,QAAQ,IACP,OAAO,EAAE,gBAAgB,EACzB,QAAQ,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,mBAAmB,CAAC,CAAC,gBAAgB,CAAC,GAC5D,EAEJ,KAAK,EAAC,0BAA0B,GAChC;YACD,CAAC,MAAM,CAAC,CAAC,CAAC,CACT;gBACE,oBAAC,iBAAiB,IAChB,OAAO,EACL,oBAAC,QAAQ,IACP,OAAO,EAAE,oBAAoB,EAC7B,QAAQ,EAAE,GAAG,EAAE,CACb,KAAK,CAAC,uBAAuB,CAAC,CAAC,oBAAoB,CAAC,GAEtD,EAEJ,KAAK,EAAC,mCAAmC,GACzC;gBACD,CAAC,oBAAoB,CAAC,CAAC,CAAC,CACvB,6BAAK,SAAS,EAAE,OAAO,CAAC,IAAI;oBAC1B,oBAAC,UAAU;;wBAAc,SAAS;8BAAiB;oBACnD,oBAAC,MAAM,IACL,SAAS,EAAE,OAAO,CAAC,KAAK,EACxB,GAAG,EAAE,EAAE,EACP,GAAG,EAAE,GAAG,EACR,KAAK,EAAE,SAAS,EAChB,QAAQ,EAAE,CAAC,CAAC,EAAE,GAAG,EAAE,EAAE,CAAC,KAAK,CAAC,YAAY,CAAC,GAAa,CAAC,GACvD,CACE,CACP,CAAC,CAAC,CAAC,IAAI,CACJ,CACP,CAAC,CAAC,CAAC,IAAI,CACJ;QACN;YACE,8CAAoB;YAEpB,oBAAC,iBAAiB,IAChB,OAAO,EACL,oBAAC,QAAQ,IACP,OAAO,EAAE,OAAO,EAChB,QAAQ,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,UAAU,CAAC,CAAC,OAAO,CAAC,GAC1C,EAEJ,KAAK,EAAC,gCAAgC,GACtC;YAEF,6BAAK,SAAS,EAAE,OAAO,CAAC,IAAI;gBAC1B,oBAAC,UAAU;;oBAAgB,QAAQ;0BAAiB;gBACpD,oBAAC,MAAM,IACL,SAAS,EAAE,OAAO,CAAC,KAAK,EACxB,GAAG,EAAE,CAAC,EACN,GAAG,EAAE,EAAE,EACP,KAAK,EAAE,QAAQ,EACf,QAAQ,EAAE,CAAC,CAAC,EAAE,GAAG,EAAE,EAAE,CAAC,KAAK,CAAC,WAAW,CAAC,GAAa,CAAC,GACtD,CACE;YACN,6BAAK,SAAS,EAAE,OAAO,CAAC,IAAI;gBAC1B,oBAAC,UAAU;;oBAAc,SAAS;0BAAiB;gBACnD,oBAAC,MAAM,IACL,SAAS,EAAE,OAAO,CAAC,KAAK,EACxB,GAAG,EAAE,CAAC,EACN,GAAG,EAAE,EAAE,EACP,KAAK,EAAE,SAAS,EAChB,QAAQ,EAAE,CAAC,CAAC,EAAE,GAAG,EAAE,EAAE,CAAC,KAAK,CAAC,YAAY,CAAC,GAAa,CAAC,GACvD,CACE;YAEN,oBAAC,SAAS,IACR,MAAM,QACN,KAAK,EAAC,cAAc,EACpB,KAAK,EAAE,eAAe,EACtB,QAAQ,EAAE,KAAK,CAAC,EAAE,CAAC,KAAK,CAAC,kBAAkB,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,IAE9D,MAAM,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE,CAAC,CACvC,oBAAC,QAAQ,IAAC,GAAG,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,IACjC,MAAM,CACE,CACZ,CAAC,CACQ,CACR,CACL,CACJ,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,MAAM,cAAc,GAAG,QAAQ,CAAC,UAAU,EACxC,KAAK,EACL,OAAO,GAIR;IACC,OAAO,CACL,oBAAC,MAAM,IAAC,IAAI,QAAC,OAAO,EAAE,GAAG,EAAE,CAAC,OAAO,EAAE,EAAE,KAAK,EAAC,UAAU;QACrD,oBAAC,aAAa;YACZ,oBAAC,eAAe,IAAC,KAAK,EAAE,KAAK,GAAI;YACjC,oBAAC,aAAa;gBACZ,oBAAC,MAAM,IAAC,OAAO,EAAE,GAAG,EAAE,CAAC,OAAO,EAAE,EAAE,OAAO,EAAC,WAAW,EAAC,KAAK,EAAC,SAAS,aAE5D,CACK,CACF,CACT,CACV,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,cAAc,CAAA"}
package/dist/model.d.ts CHANGED
@@ -2,6 +2,11 @@ import React from 'react';
2
2
  import { Instance, SnapshotIn } from 'mobx-state-tree';
3
3
  import { HierarchyNode } from 'd3-hierarchy';
4
4
  import { FileLocation as FileLocationType } from '@jbrowse/core/util/types';
5
+ import { NodeWithIds, NodeWithIdsAndLength } from './util';
6
+ import ClustalMSA from './parsers/ClustalMSA';
7
+ import StockholmMSA from './parsers/StockholmMSA';
8
+ import FastaMSA from './parsers/FastaMSA';
9
+ import { StructureModel } from './StructureModel';
5
10
  export interface RowDetails {
6
11
  [key: string]: unknown;
7
12
  name: string;
@@ -10,17 +15,17 @@ export interface RowDetails {
10
15
  end: number;
11
16
  };
12
17
  }
13
- import { NodeWithIds, NodeWithIdsAndLength } from './util';
14
- import ClustalMSA from './parsers/ClustalMSA';
15
- import StockholmMSA from './parsers/StockholmMSA';
16
- import FastaMSA from './parsers/FastaMSA';
17
- import { StructureModel } from './StructureModel';
18
18
  interface BasicTrackModel {
19
19
  id: string;
20
20
  name: string;
21
21
  associatedRowName?: string;
22
22
  height: number;
23
23
  }
24
+ interface Structure {
25
+ pdb: string;
26
+ startPos: number;
27
+ endPos: number;
28
+ }
24
29
  export interface TextTrackModel extends BasicTrackModel {
25
30
  customColorScheme?: Record<string, string>;
26
31
  data: string;
@@ -56,10 +61,6 @@ declare const model: import("mobx-state-tree").IModelType<{
56
61
  rowHeight: import("mobx-state-tree").IType<number | undefined, number, number>;
57
62
  scrollY: import("mobx-state-tree").IType<number | undefined, number, number>;
58
63
  scrollX: import("mobx-state-tree").IType<number | undefined, number, number>;
59
- resizeHandleWidth: import("mobx-state-tree").IType<number | undefined, number, number>;
60
- blockSize: import("mobx-state-tree").IType<number | undefined, number, number>;
61
- mouseRow: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
62
- mouseCol: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
63
64
  selectedStructures: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
64
65
  id: import("mobx-state-tree").ISimpleType<string>;
65
66
  structure: import("mobx-state-tree").IModelType<{
@@ -78,6 +79,11 @@ declare const model: import("mobx-state-tree").IModelType<{
78
79
  highResScaleFactor: import("mobx-state-tree").IType<number | undefined, number, number>;
79
80
  colorSchemeName: import("mobx-state-tree").IType<string | undefined, string, string>;
80
81
  treeFilehandle: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISnapshotProcessor<import("mobx-state-tree").ITypeUnion<import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
82
+ /**
83
+ * #property
84
+ * high resolution scale factor, helps make canvas look better on hi-dpi
85
+ * screens
86
+ */
81
87
  locationType: import("mobx-state-tree").ISimpleType<"UriLocation">;
82
88
  uri: import("mobx-state-tree").ISimpleType<string>;
83
89
  baseUri: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
@@ -117,20 +123,29 @@ declare const model: import("mobx-state-tree").IModelType<{
117
123
  localPath: import("mobx-state-tree").ISimpleType<string>;
118
124
  }, {}> | ({
119
125
  locationType: "UriLocation";
120
- uri: string;
126
+ uri: string; /**
127
+ * #volatile
128
+ * the currently mouse-hovered row
129
+ */
121
130
  } & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
122
131
  locationType: import("mobx-state-tree").ISimpleType<"UriLocation">;
123
132
  uri: import("mobx-state-tree").ISimpleType<string>;
124
133
  baseUri: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
125
- internetAccountId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>; /**
126
- * #action
127
- */
134
+ internetAccountId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
128
135
  internetAccountPreAuthorization: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
129
136
  internetAccountType: import("mobx-state-tree").ISimpleType<string>;
130
137
  authInfo: import("mobx-state-tree").IType<any, any, any>;
131
- }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
138
+ }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>; /**
139
+ * #action
140
+ * set the height of the view in px
141
+ */
132
142
  }>> & import("mobx-state-tree/dist/internal").NonEmptyObject)>, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
133
143
  msaFilehandle: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISnapshotProcessor<import("mobx-state-tree").ITypeUnion<import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
144
+ /**
145
+ * #property
146
+ * high resolution scale factor, helps make canvas look better on hi-dpi
147
+ * screens
148
+ */
134
149
  locationType: import("mobx-state-tree").ISimpleType<"UriLocation">;
135
150
  uri: import("mobx-state-tree").ISimpleType<string>;
136
151
  baseUri: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
@@ -170,20 +185,29 @@ declare const model: import("mobx-state-tree").IModelType<{
170
185
  localPath: import("mobx-state-tree").ISimpleType<string>;
171
186
  }, {}> | ({
172
187
  locationType: "UriLocation";
173
- uri: string;
188
+ uri: string; /**
189
+ * #volatile
190
+ * the currently mouse-hovered row
191
+ */
174
192
  } & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
175
193
  locationType: import("mobx-state-tree").ISimpleType<"UriLocation">;
176
194
  uri: import("mobx-state-tree").ISimpleType<string>;
177
195
  baseUri: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
178
- internetAccountId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>; /**
179
- * #action
180
- */
196
+ internetAccountId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
181
197
  internetAccountPreAuthorization: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
182
198
  internetAccountType: import("mobx-state-tree").ISimpleType<string>;
183
199
  authInfo: import("mobx-state-tree").IType<any, any, any>;
184
- }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
200
+ }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>; /**
201
+ * #action
202
+ * set the height of the view in px
203
+ */
185
204
  }>> & import("mobx-state-tree/dist/internal").NonEmptyObject)>, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
186
205
  treeMetadataFilehandle: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISnapshotProcessor<import("mobx-state-tree").ITypeUnion<import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
206
+ /**
207
+ * #property
208
+ * high resolution scale factor, helps make canvas look better on hi-dpi
209
+ * screens
210
+ */
187
211
  locationType: import("mobx-state-tree").ISimpleType<"UriLocation">;
188
212
  uri: import("mobx-state-tree").ISimpleType<string>;
189
213
  baseUri: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
@@ -223,21 +247,26 @@ declare const model: import("mobx-state-tree").IModelType<{
223
247
  localPath: import("mobx-state-tree").ISimpleType<string>;
224
248
  }, {}> | ({
225
249
  locationType: "UriLocation";
226
- uri: string;
250
+ uri: string; /**
251
+ * #volatile
252
+ * the currently mouse-hovered row
253
+ */
227
254
  } & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
228
255
  locationType: import("mobx-state-tree").ISimpleType<"UriLocation">;
229
256
  uri: import("mobx-state-tree").ISimpleType<string>;
230
257
  baseUri: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
231
- internetAccountId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>; /**
232
- * #action
233
- */
258
+ internetAccountId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
234
259
  internetAccountPreAuthorization: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
235
260
  internetAccountType: import("mobx-state-tree").ISimpleType<string>;
236
261
  authInfo: import("mobx-state-tree").IType<any, any, any>;
237
- }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
262
+ }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>; /**
263
+ * #action
264
+ * set the height of the view in px
265
+ */
238
266
  }>> & import("mobx-state-tree/dist/internal").NonEmptyObject)>, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
239
267
  currentAlignment: import("mobx-state-tree").IType<number | undefined, number, number>;
240
268
  collapsed: import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>;
269
+ hidden: import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>;
241
270
  showOnly: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
242
271
  boxTracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
243
272
  id: import("mobx-state-tree").ISimpleType<string>;
@@ -267,11 +296,6 @@ declare const model: import("mobx-state-tree").IModelType<{
267
296
  }[] | undefined;
268
297
  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
269
298
  turnedOffTracks: import("mobx-state-tree").IMapType<import("mobx-state-tree").ISimpleType<boolean>>;
270
- annotatedRegions: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
271
- start: import("mobx-state-tree").ISimpleType<number>;
272
- end: import("mobx-state-tree").ISimpleType<number>;
273
- attributes: import("mobx-state-tree").IType<Record<string, string[]>, Record<string, string[]>, Record<string, string[]>>;
274
- }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
275
299
  data: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
276
300
  tree: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
277
301
  msa: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
@@ -298,6 +322,26 @@ declare const model: import("mobx-state-tree").IModelType<{
298
322
  removeActiveDialog(): void;
299
323
  queueDialog(cb: (doneCallback: () => void) => [import("@jbrowse/core/util").DialogComponentType, unknown]): void;
300
324
  } & {
325
+ /**
326
+ * #volatile
327
+ * resize handle width between tree and msa area, px
328
+ */
329
+ resizeHandleWidth: number;
330
+ /**
331
+ * #volatile
332
+ * size of blocks of content to be drawn, px
333
+ */
334
+ blockSize: number;
335
+ /**
336
+ * #volatile
337
+ * the currently mouse-hovered row
338
+ */
339
+ mouseRow: number | undefined;
340
+ /**
341
+ * #volatile
342
+ * the currently mouse-hovered column
343
+ */
344
+ mouseCol: number | undefined;
301
345
  /**
302
346
  * #volatile
303
347
  * a dummy variable that is incremented when ref changes so autorun for
@@ -329,18 +373,22 @@ declare const model: import("mobx-state-tree").IModelType<{
329
373
  } & {
330
374
  /**
331
375
  * #action
376
+ * set the height of the view in px
332
377
  */
333
378
  setHeight(height: number): void;
334
379
  /**
335
380
  * #action
381
+ * add to the selected structures
336
382
  */
337
383
  addStructureToSelection(elt: StructureSnap): void;
338
384
  /**
339
385
  * #action
386
+ * remove from the selected structures
340
387
  */
341
388
  removeStructureFromSelection(elt: StructureSnap): void;
342
389
  /**
343
390
  * #action
391
+ * toggle a structure from the selected structures list
344
392
  */
345
393
  toggleStructureSelection(elt: {
346
394
  id: string;
@@ -352,46 +400,57 @@ declare const model: import("mobx-state-tree").IModelType<{
352
400
  }): void;
353
401
  /**
354
402
  * #action
403
+ * clear all selected structures
355
404
  */
356
405
  clearSelectedStructures(): void;
357
406
  /**
358
407
  * #action
408
+ * set error state
359
409
  */
360
410
  setError(error?: unknown): void;
361
411
  /**
362
412
  * #action
413
+ * set mouse position (row, column) in the MSA
363
414
  */
364
415
  setMousePos(col?: number, row?: number): void;
365
416
  /**
366
417
  * #action
418
+ * set row height (px)
367
419
  */
368
420
  setRowHeight(n: number): void;
369
421
  /**
370
422
  * #action
423
+ * set col width (px)
371
424
  */
372
425
  setColWidth(n: number): void;
373
426
  /**
374
427
  * #action
428
+ * set color scheme name
375
429
  */
376
430
  setColorSchemeName(name: string): void;
377
431
  /**
378
432
  * #action
433
+ * synchronize the treewidth and treeareawidth
379
434
  */
380
435
  setTreeWidthMatchesArea(arg: boolean): void;
381
436
  /**
382
437
  * #action
438
+ * set scroll Y-offset (px)
383
439
  */
384
440
  setScrollY(n: number): void;
385
441
  /**
386
442
  * #action
443
+ * set tree area width (px)
387
444
  */
388
445
  setTreeAreaWidth(n: number): void;
389
446
  /**
390
447
  * #action
448
+ * set tree width (px)
391
449
  */
392
450
  setTreeWidth(n: number): void;
393
451
  /**
394
452
  * #action
453
+ *
395
454
  */
396
455
  setCurrentAlignment(n: number): void;
397
456
  /**
@@ -402,6 +461,14 @@ declare const model: import("mobx-state-tree").IModelType<{
402
461
  * #action
403
462
  */
404
463
  setDrawTree(arg: boolean): void;
464
+ /**
465
+ * #action
466
+ */
467
+ hideNode(arg: string): void;
468
+ /**
469
+ * #action
470
+ */
471
+ clearHidden(): void;
405
472
  /**
406
473
  * #action
407
474
  */
@@ -524,14 +591,15 @@ declare const model: import("mobx-state-tree").IModelType<{
524
591
  /**
525
592
  * #getter
526
593
  */
527
- readonly tree: NodeWithIds;
594
+ readonly _tree: NodeWithIds;
528
595
  /**
529
596
  * #getter
530
597
  */
531
598
  readonly rowNames: string[];
532
599
  /**
533
600
  * #getter
534
- */ readonly mouseOverRowName: string | undefined;
601
+ */
602
+ readonly mouseOverRowName: string | undefined;
535
603
  /**
536
604
  * #method
537
605
  */
@@ -543,11 +611,7 @@ declare const model: import("mobx-state-tree").IModelType<{
543
611
  /**
544
612
  * #getter
545
613
  */
546
- readonly structures: Record<string, {
547
- pdb: string;
548
- startPos: number;
549
- endPos: number;
550
- }[]>;
614
+ readonly structures: Record<string, Structure[]>;
551
615
  /**
552
616
  * #getter
553
617
  */
@@ -558,6 +622,7 @@ declare const model: import("mobx-state-tree").IModelType<{
558
622
  };
559
623
  /**
560
624
  * #getter
625
+ * widget width minus the tree area gives the space for the MSA
561
626
  */
562
627
  readonly msaAreaWidth: number;
563
628
  /**
@@ -567,7 +632,7 @@ declare const model: import("mobx-state-tree").IModelType<{
567
632
  /**
568
633
  * #getter
569
634
  */
570
- readonly rows: [string, string[]][];
635
+ readonly rows: [string, string][];
571
636
  /**
572
637
  * #getter
573
638
  */
@@ -640,6 +705,14 @@ declare const model: import("mobx-state-tree").IModelType<{
640
705
  * #getter
641
706
  */
642
707
  readonly conservation: string[];
708
+ /**
709
+ * #getter
710
+ */
711
+ readonly adapterTrackModels: BasicTrack[];
712
+ /**
713
+ * #getter
714
+ */
715
+ readonly boxTrackModels: BasicTrack[];
643
716
  /**
644
717
  * #getter
645
718
  */
@@ -668,30 +741,23 @@ declare const model: import("mobx-state-tree").IModelType<{
668
741
  /**
669
742
  * #method
670
743
  */
671
- getPos(pos: number): number;
672
- } & {
673
- /**
674
- * #action
675
- */
676
- addAnnotation(start: number, end: number, attributes: Record<string, string[]>): void;
677
- /**
678
- * #action
679
- */
680
- setAnnotationClickBoundaries(left: number, right: number): void;
681
- /**
682
- * #action
683
- */
684
- clearAnnotationClickBoundaries(): void;
744
+ relativePxToBp2(rowName: string, position: number): number;
685
745
  /**
686
- * #action
746
+ * #method
687
747
  */
688
- incrementRef(): void;
748
+ getPos(pos: number): number;
689
749
  } & {
690
750
  /**
691
751
  * #getter
752
+ * total height of track area (px)
692
753
  */
693
754
  readonly totalTrackAreaHeight: number;
694
755
  } & {
756
+ /**
757
+ * #action
758
+ * internal, used for drawing to canvas
759
+ */
760
+ incrementRef(): void;
695
761
  afterCreate(): void;
696
762
  }, import("mobx-state-tree")._NotCustomized, {
697
763
  id: string;
@@ -701,8 +767,6 @@ declare const model: import("mobx-state-tree").IModelType<{
701
767
  rowHeight: number;
702
768
  scrollY: number;
703
769
  scrollX: number;
704
- resizeHandleWidth: number;
705
- blockSize: number;
706
770
  labelsAlignRight: boolean;
707
771
  colWidth: number;
708
772
  showBranchLen: boolean;
@@ -714,8 +778,6 @@ declare const model: import("mobx-state-tree").IModelType<{
714
778
  currentAlignment: number;
715
779
  treeAreaWidth: number;
716
780
  treeWidth: number;
717
- mouseRow: number | undefined;
718
- mouseCol: number | undefined;
719
781
  selectedStructures: import("mobx-state-tree").ModelSnapshotType<{
720
782
  id: import("mobx-state-tree").ISimpleType<string>;
721
783
  structure: import("mobx-state-tree").IModelType<{
@@ -774,6 +836,7 @@ declare const model: import("mobx-state-tree").IModelType<{
774
836
  localPath: import("mobx-state-tree").ISimpleType<string>;
775
837
  }> | undefined;
776
838
  collapsed: string[];
839
+ hidden: string[];
777
840
  showOnly: string | undefined;
778
841
  boxTracks: import("mobx-state-tree").ModelSnapshotType<{
779
842
  id: import("mobx-state-tree").ISimpleType<string>;
@@ -783,11 +846,6 @@ declare const model: import("mobx-state-tree").IModelType<{
783
846
  height: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
784
847
  }>[];
785
848
  turnedOffTracks: import("mobx").IKeyValueMap<boolean>;
786
- annotatedRegions: import("mobx-state-tree").ModelSnapshotType<{
787
- start: import("mobx-state-tree").ISimpleType<number>;
788
- end: import("mobx-state-tree").ISimpleType<number>;
789
- attributes: import("mobx-state-tree").IType<Record<string, string[]>, Record<string, string[]>, Record<string, string[]>>;
790
- }>[];
791
849
  displayName: string | undefined;
792
850
  minimized: boolean;
793
851
  data: {