jbrowse-plugin-msaview 5.6.0 → 5.8.0

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Files changed (100) hide show
  1. package/dist/MsaViewPanel/model.d.ts +79 -43
  2. package/dist/chunks/{AboutDialog-HCCCEJ6V.js → AboutDialog-N23GOSSA.js} +2 -2
  3. package/dist/chunks/{AboutDialog-HCCCEJ6V.js.map → AboutDialog-N23GOSSA.js.map} +1 -1
  4. package/dist/chunks/AnnotationFileDialog-FVQNLVEU.js +2 -0
  5. package/dist/chunks/AnnotationFileDialog-FVQNLVEU.js.map +7 -0
  6. package/dist/chunks/{ExportSVGDialog-YUFLYBYW.js → ExportSVGDialog-3SA6HFZB.js} +2 -2
  7. package/dist/chunks/{ExportSVGDialog-YUFLYBYW.js.map → ExportSVGDialog-3SA6HFZB.js.map} +1 -1
  8. package/dist/chunks/{FeatureDialog-NBDB5SWU.js → FeatureDialog-LSD37OFH.js} +2 -2
  9. package/dist/chunks/{FeatureDialog-NBDB5SWU.js.map → FeatureDialog-LSD37OFH.js.map} +3 -3
  10. package/dist/chunks/GapThresholdDialog-TD527ERL.js +2 -0
  11. package/dist/chunks/GapThresholdDialog-TD527ERL.js.map +7 -0
  12. package/dist/chunks/GoToDialog-M5ICFHVT.js +2 -0
  13. package/dist/chunks/GoToDialog-M5ICFHVT.js.map +7 -0
  14. package/dist/chunks/{HelpDialog-UCUYPCOI.js → HelpDialog-KB7HMUOR.js} +2 -2
  15. package/dist/chunks/{HelpDialog-UCUYPCOI.js.map → HelpDialog-KB7HMUOR.js.map} +1 -1
  16. package/dist/chunks/{LaunchMsaViewDialog-BG4MX2BW.js → LaunchMsaViewDialog-GR4BB3W2.js} +2 -2
  17. package/dist/chunks/{LaunchMsaViewDialog-BG4MX2BW.js.map → LaunchMsaViewDialog-GR4BB3W2.js.map} +1 -1
  18. package/dist/chunks/MetadataDialog-CM2V36UG.js +2 -0
  19. package/dist/chunks/MetadataDialog-CM2V36UG.js.map +7 -0
  20. package/dist/chunks/MsaViewPanel-YVMUOMSJ.js +2 -0
  21. package/dist/chunks/{MsaViewPanel-XSXFJWWY.js.map → MsaViewPanel-YVMUOMSJ.js.map} +1 -1
  22. package/dist/chunks/{TrackInfoDialog-YXCIGFYM.js → TrackInfoDialog-KAER67NZ.js} +2 -2
  23. package/dist/chunks/{TrackInfoDialog-YXCIGFYM.js.map → TrackInfoDialog-KAER67NZ.js.map} +1 -1
  24. package/dist/chunks/TreeNodeInfoDialog-G4NOFRUB.js +2 -0
  25. package/dist/chunks/{TreeNodeInfoDialog-QCWDJTM4.js.map → TreeNodeInfoDialog-G4NOFRUB.js.map} +2 -2
  26. package/dist/chunks/chunk-6GRHBYHB.js +6 -0
  27. package/dist/chunks/chunk-6GRHBYHB.js.map +7 -0
  28. package/dist/chunks/chunk-7ZQPYLN2.js +2 -0
  29. package/dist/chunks/chunk-7ZQPYLN2.js.map +7 -0
  30. package/dist/chunks/chunk-A6AI2XFP.js +2 -0
  31. package/dist/chunks/chunk-A6AI2XFP.js.map +7 -0
  32. package/dist/chunks/chunk-BICRHYID.js +164 -0
  33. package/dist/chunks/chunk-BICRHYID.js.map +7 -0
  34. package/dist/chunks/chunk-CH7JHGQF.js +2 -0
  35. package/dist/chunks/chunk-CH7JHGQF.js.map +7 -0
  36. package/dist/chunks/{chunk-35FWLG3N.js → chunk-DN4LFP5T.js} +1 -1
  37. package/dist/chunks/{chunk-35FWLG3N.js.map → chunk-DN4LFP5T.js.map} +1 -1
  38. package/dist/chunks/{chunk-5OSSOQH4.js → chunk-DXB6E5M4.js} +1 -1
  39. package/dist/chunks/{chunk-5OSSOQH4.js.map → chunk-DXB6E5M4.js.map} +1 -1
  40. package/dist/chunks/{chunk-4TEPHD3L.js → chunk-DYDEKAIN.js} +2 -2
  41. package/dist/chunks/{chunk-KSCGTF4R.js → chunk-EKTRLQV7.js} +2 -2
  42. package/dist/chunks/chunk-J2OCCRDG.js +6 -0
  43. package/dist/chunks/chunk-J2OCCRDG.js.map +7 -0
  44. package/dist/chunks/chunk-K55ZVN73.js +5 -0
  45. package/dist/chunks/chunk-K55ZVN73.js.map +7 -0
  46. package/dist/chunks/chunk-KYQ2SO7B.js +2 -0
  47. package/dist/chunks/{chunk-QQKPT6EL.js.map → chunk-KYQ2SO7B.js.map} +1 -1
  48. package/dist/chunks/{chunk-NLAW2OYS.js → chunk-M2AAIXY5.js} +2 -2
  49. package/dist/chunks/{chunk-AQ2THRTR.js → chunk-QWXSEUZI.js} +2 -2
  50. package/dist/chunks/{chunk-GAY2PLS6.js → chunk-RFKEQQMZ.js} +1 -1
  51. package/dist/chunks/{chunk-GAY2PLS6.js.map → chunk-RFKEQQMZ.js.map} +1 -1
  52. package/dist/chunks/chunk-SYZYE3AS.js +2 -0
  53. package/dist/chunks/chunk-SYZYE3AS.js.map +7 -0
  54. package/dist/chunks/chunk-WNIBTLFE.js +2 -0
  55. package/dist/chunks/{chunk-XTQQNBQ5.js.map → chunk-WNIBTLFE.js.map} +2 -2
  56. package/dist/chunks/chunk-XZBGVA3Q.js +8 -0
  57. package/dist/chunks/chunk-XZBGVA3Q.js.map +7 -0
  58. package/dist/chunks/{chunk-666BV764.js → chunk-YLUFN5D7.js} +2 -2
  59. package/dist/chunks/{chunk-666BV764.js.map → chunk-YLUFN5D7.js.map} +1 -1
  60. package/dist/chunks/dist-OFRIFLPB.js +2 -0
  61. package/dist/chunks/{dist-GXYZN4ZR.js → dist-QVW6GF25.js} +1 -1
  62. package/dist/chunks/{dist-GXYZN4ZR.js.map → dist-QVW6GF25.js.map} +1 -1
  63. package/dist/chunks/{model-SEEQQSQO.js → model-GRN6F5EO.js} +2 -2
  64. package/dist/chunks/{model-SEEQQSQO.js.map → model-GRN6F5EO.js.map} +1 -1
  65. package/dist/chunks/{renderToSvg-5DMIQ72S.js → renderToSvg-DDCUEDRY.js} +2 -2
  66. package/dist/jbrowse-plugin-msaview.esm.js +2 -2
  67. package/dist/jbrowse-plugin-msaview.esm.js.map +1 -1
  68. package/dist/version.d.ts +1 -1
  69. package/dist/version.js +1 -1
  70. package/package.json +2 -2
  71. package/src/version.ts +1 -1
  72. package/dist/chunks/AnnotationFileDialog-CPJ4X7XW.js +0 -2
  73. package/dist/chunks/AnnotationFileDialog-CPJ4X7XW.js.map +0 -7
  74. package/dist/chunks/MetadataDialog-DSA3545E.js +0 -2
  75. package/dist/chunks/MetadataDialog-DSA3545E.js.map +0 -7
  76. package/dist/chunks/MsaViewPanel-XSXFJWWY.js +0 -2
  77. package/dist/chunks/TreeNodeInfoDialog-QCWDJTM4.js +0 -2
  78. package/dist/chunks/chunk-ASUKJX5J.js +0 -2
  79. package/dist/chunks/chunk-ASUKJX5J.js.map +0 -7
  80. package/dist/chunks/chunk-F726IWCW.js +0 -2
  81. package/dist/chunks/chunk-F726IWCW.js.map +0 -7
  82. package/dist/chunks/chunk-FFHB7WP7.js +0 -18
  83. package/dist/chunks/chunk-FFHB7WP7.js.map +0 -7
  84. package/dist/chunks/chunk-JDQUBCHM.js +0 -2
  85. package/dist/chunks/chunk-JDQUBCHM.js.map +0 -7
  86. package/dist/chunks/chunk-QQKPT6EL.js +0 -2
  87. package/dist/chunks/chunk-WMDOEOAH.js +0 -6
  88. package/dist/chunks/chunk-WMDOEOAH.js.map +0 -7
  89. package/dist/chunks/chunk-XTQQNBQ5.js +0 -2
  90. package/dist/chunks/chunk-XXCNVFGP.js +0 -11
  91. package/dist/chunks/chunk-XXCNVFGP.js.map +0 -7
  92. package/dist/chunks/chunk-ZQSWX57C.js +0 -2
  93. package/dist/chunks/chunk-ZQSWX57C.js.map +0 -7
  94. package/dist/chunks/dist-GZKCGB2N.js +0 -2
  95. /package/dist/chunks/{chunk-4TEPHD3L.js.map → chunk-DYDEKAIN.js.map} +0 -0
  96. /package/dist/chunks/{chunk-KSCGTF4R.js.map → chunk-EKTRLQV7.js.map} +0 -0
  97. /package/dist/chunks/{chunk-NLAW2OYS.js.map → chunk-M2AAIXY5.js.map} +0 -0
  98. /package/dist/chunks/{chunk-AQ2THRTR.js.map → chunk-QWXSEUZI.js.map} +0 -0
  99. /package/dist/chunks/{dist-GZKCGB2N.js.map → dist-OFRIFLPB.js.map} +0 -0
  100. /package/dist/chunks/{renderToSvg-5DMIQ72S.js.map → renderToSvg-DDCUEDRY.js.map} +0 -0
@@ -112,7 +112,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
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  id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
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  displayName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
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  minimized: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
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- }, "id" | "type" | "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "treeAreaWidth" | "treeOrder" | "treeWidth" | "bgColor" | "colorSchemeName" | "customColorScheme" | "msaFormat" | "showColumnStats" | "allowedGappyness" | "clades" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "drawMsaLetters" | "encodings" | "features" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "msaFilehandle" | "region" | "relativeTo" | "residueMappings" | "rotated" | "rowHeight" | "rowPanels" | "scrollX" | "scrollY" | "scrollZoom" | "scrollZoomAxis" | "selection" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "trackHeights" | "treeFilehandle" | "treeMetadataFilehandle" | "treeRoot" | "turnedOffFeatures" | "turnedOffTracks"> & Omit<Omit<Omit<{}, "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "treeAreaWidth" | "treeOrder" | "treeWidth"> & {
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+ }, "id" | "type" | "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "showTreeScaleBar" | "treeAreaWidth" | "treeOrder" | "treeWidth" | "bgColor" | "colorSchemeName" | "customColorScheme" | "msaFormat" | "showColumnStats" | "allowedGappyness" | "clades" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "domainFill" | "drawMsaLetters" | "embeddedMode" | "encodings" | "features" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "msaFilehandle" | "region" | "relativeTo" | "residueMappings" | "rotated" | "rowHeight" | "rowPanels" | "scrollX" | "scrollY" | "scrollZoom" | "scrollZoomAxis" | "selection" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "trackHeights" | "treeFilehandle" | "treeMetadataFilehandle" | "treeRoot" | "turnedOffFeatures" | "turnedOffTracks"> & Omit<Omit<Omit<{}, "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "showTreeScaleBar" | "treeAreaWidth" | "treeOrder" | "treeWidth"> & {
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  drawLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
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  labelsAlignRight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
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  treeAreaWidth: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
@@ -123,22 +123,25 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
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  drawNodeBubbles: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
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  drawNodeLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
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  showTreeOverview: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
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+ showTreeScaleBar: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
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  overviewHeight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
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  }, "bgColor" | "colorSchemeName" | "customColorScheme" | "msaFormat" | "showColumnStats"> & {
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  bgColor: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
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  colorSchemeName: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
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  customColorScheme: import("@jbrowse/mobx-state-tree").IType<Record<string, string> | undefined, Record<string, string> | undefined, Record<string, string> | undefined>;
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  showColumnStats: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
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- msaFormat: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<import("msa-parsers").MSAFormat>>;
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- }, "id" | "type" | "allowedGappyness" | "clades" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "drawMsaLetters" | "encodings" | "features" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "msaFilehandle" | "region" | "relativeTo" | "residueMappings" | "rotated" | "rowHeight" | "rowPanels" | "scrollX" | "scrollY" | "scrollZoom" | "scrollZoomAxis" | "selection" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "trackHeights" | "treeFilehandle" | "treeMetadataFilehandle" | "treeRoot" | "turnedOffFeatures" | "turnedOffTracks"> & {
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+ msaFormat: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<import("react-msaview").MSAFormat>>;
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+ }, "id" | "type" | "allowedGappyness" | "clades" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "domainFill" | "drawMsaLetters" | "embeddedMode" | "encodings" | "features" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "msaFilehandle" | "region" | "relativeTo" | "residueMappings" | "rotated" | "rowHeight" | "rowPanels" | "scrollX" | "scrollY" | "scrollZoom" | "scrollZoomAxis" | "selection" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "trackHeights" | "treeFilehandle" | "treeMetadataFilehandle" | "treeRoot" | "turnedOffFeatures" | "turnedOffTracks"> & {
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  id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
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  showDomains: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
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+ domainFill: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
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  showDomainLegend: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
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  hideGaps: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
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  allowedGappyness: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
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  subFeatureRows: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
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  type: import("@jbrowse/mobx-state-tree").ILiteralType<"MsaView">;
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  drawMsaLetters: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
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+ embeddedMode: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
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  scrollZoom: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
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  scrollZoomAxis: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<"both" | "horizontal" | "vertical">, [undefined]>;
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  height: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
@@ -473,7 +476,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
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  showOnly: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
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  turnedOffTracks: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>, [undefined]>;
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  trackHeights: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<number>>, [undefined]>;
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- columnTracks: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("react-msaview").ColumnTrackSpec, import("react-msaview").ColumnTrackSpec, import("react-msaview").ColumnTrackSpec>>, [undefined]>;
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+ columnTracks: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").IType<import("react-msaview").ColumnTrackSpec, import("react-msaview").ColumnTrackSpec, import("react-msaview").ColumnTrackSpec>, import("react-msaview").ColumnTrackSpec, import("@jbrowse/mobx-state-tree")._NotCustomized>>, [undefined]>;
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  residueMappings: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("react-msaview").ResidueMapping, import("react-msaview").ResidueMapping, import("react-msaview").ResidueMapping>>, [undefined]>;
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  data: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IModelType<{
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  tree: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
@@ -496,9 +499,9 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
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  selection: import("@jbrowse/mobx-state-tree").IType<import("react-msaview").MsaSelection | undefined, import("react-msaview").MsaSelection | undefined, import("react-msaview").MsaSelection | undefined>;
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  region: import("@jbrowse/mobx-state-tree").IType<import("react-msaview").Region | undefined, import("react-msaview").Region | undefined, import("react-msaview").Region | undefined>;
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  clades: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("react-msaview").Clade, import("react-msaview").Clade, import("react-msaview").Clade>>, [undefined]>;
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- encodings: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("react-msaview").Encoding, import("react-msaview").Encoding, import("react-msaview").Encoding>>, [undefined]>;
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- rowPanels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("react-msaview").RowPanelSpec, import("react-msaview").RowPanelSpec, import("react-msaview").RowPanelSpec>>, [undefined]>;
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- }, "init" | "querySeqName" | "launchCompleted" | "embeddedMode" | "connectedViewId" | "connectedFeature" | "connectedTranscript" | "blastParams" | "orthologParams" | "querySeqOffset" | "uniprotId" | "zoomToBaseLevel" | "dataStoreId" | "mafRegion" | "domainsOnGenome"> & {
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+ encodings: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").IType<import("react-msaview").Encoding, import("react-msaview").Encoding, import("react-msaview").Encoding>, import("react-msaview").Encoding | import("react-msaview").LegacyEncoding, import("@jbrowse/mobx-state-tree")._NotCustomized>>, [undefined]>;
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+ rowPanels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").IType<import("react-msaview").RowPanelSpec, import("react-msaview").RowPanelSpec, import("react-msaview").RowPanelSpec>, import("react-msaview").LegacyRowPanel | import("react-msaview").RowPanelSpec, import("@jbrowse/mobx-state-tree")._NotCustomized>>, [undefined]>;
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+ }, "init" | "querySeqName" | "embeddedMode" | "launchCompleted" | "connectedViewId" | "connectedFeature" | "connectedTranscript" | "blastParams" | "orthologParams" | "querySeqOffset" | "uniprotId" | "zoomToBaseLevel" | "dataStoreId" | "mafRegion" | "domainsOnGenome"> & {
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  connectedViewId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
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  connectedFeature: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
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  connectedTranscript: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
@@ -546,15 +549,21 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
546
549
  setDrawNodeBubbles(arg: boolean): void;
547
550
  setDrawNodeLabels(arg: boolean): void;
548
551
  setShowTreeOverview(arg: boolean): void;
552
+ setShowTreeScaleBar(arg: boolean): void;
549
553
  setDrawLabels(arg: boolean): void;
550
554
  } & {
551
555
  setColorSchemeName(name: string): void;
552
556
  setCustomColorScheme(map?: Record<string, string>): void;
553
557
  setBgColor(arg: boolean): void;
554
558
  setShowColumnStats(arg: boolean): void;
555
- setMSAFormat(arg?: import("msa-parsers").MSAFormat): void;
559
+ setMSAFormat(arg?: import("react-msaview").MSAFormat): void;
556
560
  } & {
557
561
  headerHeight: number;
562
+ settingsOpen: boolean;
563
+ zoomHeld: {
564
+ col: number;
565
+ row: number;
566
+ };
558
567
  hideHeader: boolean;
559
568
  importForm: boolean;
560
569
  status: {
@@ -562,6 +571,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
562
571
  onCancel?: () => void;
563
572
  } | undefined;
564
573
  highResScaleFactor: number;
574
+ zoomSnapshot: import("react-msaview").ZoomSnapshot | undefined;
565
575
  loadingMSA: boolean;
566
576
  loadingTree: boolean;
567
577
  volatileWidth: number | undefined;
@@ -584,7 +594,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
584
594
  dismissedWarnings: string[];
585
595
  resetCount: number;
586
596
  hostCarriesData: boolean;
587
- annotations: import("msa-parsers").Annotation[];
597
+ annotations: import("react-msaview").Annotation[];
588
598
  } & {
589
599
  drawRelativeTo(id: string | undefined): void;
590
600
  setHideGaps(arg: boolean): void;
@@ -592,6 +602,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
592
602
  setLoadingMSA(arg: boolean): void;
593
603
  setLoadingTree(arg: boolean): void;
594
604
  setWidth(arg: number): void;
605
+ setSettingsOpen(arg: boolean): void;
595
606
  setHighResScaleFactor(arg: number): void;
596
607
  setHeight(height: number): void;
597
608
  setError(error?: unknown): void;
@@ -608,6 +619,8 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
608
619
  applyHighlight(owner: string, highlights: import("react-msaview").Highlight[]): void;
609
620
  clearHighlight(owner: string): void;
610
621
  setShowDomains(arg: boolean): void;
622
+ setDomainFill(arg: boolean): void;
623
+ setCellFill(mode: "residue" | "domain" | "none"): void;
611
624
  setShowDomainLegend(arg: boolean): void;
612
625
  setSubFeatureRows(arg: boolean): void;
613
626
  setMouseClickPos(col?: number, row?: number): void;
@@ -635,8 +648,6 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
635
648
  setGFF(result?: string): void;
636
649
  } & {
637
650
  readonly hideGapsEffective: boolean;
638
- readonly allAnnotations: import("msa-parsers").Annotation[];
639
- readonly actuallyShowDomains: boolean;
640
651
  readonly hostRestoresData: boolean;
641
652
  readonly viewInitialized: boolean;
642
653
  readonly width: number;
@@ -663,7 +674,9 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
663
674
  readonly rowData: Record<string, Record<string, string> | undefined>;
664
675
  rowDataOf(name: string): Record<string, string> | undefined;
665
676
  readonly rowFields: string[];
666
- readonly MSA: import("msa-parsers").MSAParserType | null;
677
+ readonly MSA: import("react-msaview").MSAParserType | null;
678
+ readonly allAnnotations: import("react-msaview").Annotation[];
679
+ readonly actuallyShowDomains: boolean;
667
680
  readonly numColumns: number;
668
681
  readonly inputTree: import("react-msaview").NodeWithIds;
669
682
  readonly tree: import("react-msaview").NodeWithIds;
@@ -727,6 +740,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
727
740
  color: string | undefined;
728
741
  }[];
729
742
  readonly colClustalX: Record<string, string>[];
743
+ readonly colSimilarity: Record<string, string>[];
730
744
  readonly conservation: number[];
731
745
  readonly alphabetMaxBits: number;
732
746
  readonly propertyConservation: number[];
@@ -762,6 +776,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
762
776
  readonly adapterTrackModels: import("react-msaview").BasicTrack[];
763
777
  readonly basePairTrackModels: import("react-msaview").BasicTrack[];
764
778
  readonly computedTrackModels: import("react-msaview").BasicTrack[];
779
+ readonly referenceTrackModels: import("react-msaview").BasicTrack[];
765
780
  readonly tracks: import("react-msaview").BasicTrack[];
766
781
  readonly turnedOnTracks: import("react-msaview").BasicTrack[];
767
782
  readonly showHorizontalScrollbar: boolean;
@@ -794,9 +809,12 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
794
809
  readonly topBandHeight: number;
795
810
  readonly msaAreaHeight: number;
796
811
  readonly totalTrackAreaHeight: number;
797
- readonly annotationTypes: Map<string, import("msa-parsers").Annotation>;
798
- readonly filteredAnnotations: import("msa-parsers").Annotation[];
799
- readonly annotationsByRow: Record<string, import("msa-parsers").Annotation[]>;
812
+ readonly annotationTypes: Map<string, import("react-msaview").Annotation>;
813
+ readonly defaultOffAccessions: Set<string>;
814
+ featureOff(accession: string): boolean;
815
+ readonly filteredAnnotations: import("react-msaview").Annotation[];
816
+ readonly cellFill: "residue" | "domain" | "none";
817
+ readonly annotationsByRow: Record<string, import("react-msaview").Annotation[]>;
800
818
  } & {
801
819
  readonly showVerticalScrollbar: boolean;
802
820
  } & {
@@ -808,6 +826,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
808
826
  readonly msaCanvasWidth: number;
809
827
  readonly maxScrollX: number;
810
828
  readonly blocks2d: (readonly [number, number])[];
829
+ readonly wheelZooming: boolean;
811
830
  readonly isLoading: boolean;
812
831
  readonly dataWarnings: string[];
813
832
  readonly warnings: string[];
@@ -827,18 +846,21 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
827
846
  zoomIn(): void;
828
847
  zoomOut(): void;
829
848
  zoomToPos(scaleFactor: number, offsetX: number, offsetY: number, axis?: "both" | "horizontal" | "vertical"): void;
849
+ wheelZoomToPos(scaleFactor: number, offsetX: number, offsetY: number): void;
850
+ endWheelZoom(): void;
830
851
  doScrollY(deltaY: number): void;
831
852
  setScrollY(n: number): void;
832
- setAnnotations(annotations: import("msa-parsers").Annotation[]): void;
853
+ setAnnotations(annotations: import("react-msaview").Annotation[]): void;
833
854
  applyGFFText(gffText: string): void;
834
855
  doScrollX(deltaX: number): void;
835
856
  setScrollX(n: number): void;
836
- setColumnTracks(tracks: import("react-msaview").ColumnTrackSpec[]): void;
857
+ setColumnTracks(tracks: (import("react-msaview").ColumnTrackSpec | import("react-msaview").LegacyColumnTrack)[]): void;
837
858
  setRowData(rowData: import("react-msaview").RowDataInput): void;
838
- setEncodings(encodings: import("react-msaview").Encoding[]): void;
839
- setRowPanels(panels: import("react-msaview").RowPanelSpec[]): void;
859
+ setEncodings(encodings: (import("react-msaview").Encoding | import("react-msaview").LegacyEncoding)[]): void;
860
+ setRowPanels(panels: (import("react-msaview").RowPanelSpec | import("react-msaview").LegacyRowPanel)[]): void;
840
861
  setResidueMappings(mappings: import("react-msaview").ResidueMapping[]): void;
841
862
  toggleTrack(id: string): void;
863
+ setTracksShown(ids: string[], shown: boolean): void;
842
864
  setStatus(status?: {
843
865
  msg: string;
844
866
  onCancel?: () => void;
@@ -848,24 +870,24 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
848
870
  readonly hoveredCell: import("react-msaview").Cell | undefined;
849
871
  readonly clickedCell: import("react-msaview").Cell | undefined;
850
872
  readonly viewport: import("react-msaview").Viewport | undefined;
851
- readonly segmentDomainTypes: import("msa-parsers").Annotation[];
852
- readonly categoricalDomainTypes: import("msa-parsers").Annotation[];
873
+ readonly segmentDomainTypes: import("react-msaview").Annotation[];
874
+ readonly categoricalDomainTypes: import("react-msaview").Annotation[];
853
875
  readonly fillPalette: {
854
876
  [x: string]: string;
855
877
  };
856
878
  readonly featureFillEncoding: import("react-msaview").ResolvedEncoding | undefined;
857
- readonly featureColors: Map<import("msa-parsers").Annotation, {
879
+ readonly featureColors: Map<import("react-msaview").Annotation, {
858
880
  fill: string;
859
881
  stroke: string;
860
882
  }>;
861
- readonly featureLabels: Map<import("msa-parsers").Annotation, string> | undefined;
883
+ readonly featureLabels: Map<import("react-msaview").Annotation, string> | undefined;
862
884
  readonly segmentLabels: Map<string, string>;
863
- readonly visibleDomainTypes: import("msa-parsers").Annotation[];
885
+ readonly visibleDomainTypes: import("react-msaview").Annotation[];
864
886
  readonly legends: import("react-msaview").Legend[];
865
887
  readonly domainUnderline: boolean;
866
888
  readonly domainBands: Map<string, import("react-msaview").DomainBand[]>;
867
889
  readonly domainBandsByStart: Map<string, import("react-msaview").DomainBand[]>;
868
- readonly mouseOverDomains: import("msa-parsers").Annotation[];
890
+ readonly mouseOverDomains: import("react-msaview").Annotation[];
869
891
  readonly referenceRowIndex: number | undefined;
870
892
  readonly hoveredRowIndices: number[];
871
893
  readonly highlightedColumnRuns: {
@@ -894,25 +916,29 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
894
916
  rowData: Record<string, string> | undefined;
895
917
  };
896
918
  readonly resolvedEncodings: import("react-msaview").ResolvedEncoding[];
919
+ readonly resolvedScales: Map<string, import("react-msaview").SharedScale>;
920
+ scaleOf(channel: import("react-msaview").ColorChannel, table: import("react-msaview").ScaleTable): import("react-msaview").SharedScale;
897
921
  readonly rowPanelScales: ({
898
922
  header: string;
899
- kind: "strip";
900
923
  field: string;
901
- colors: Map<string, string>;
924
+ kind: "strip";
902
925
  legend: import("react-msaview").LegendEntry[];
926
+ colors: Map<string, string>;
927
+ legendKey?: string | undefined;
903
928
  legendTitle?: string | undefined;
904
929
  } | {
905
930
  header: string;
906
931
  x: "column" | "position";
907
- kind: "features";
908
932
  field?: string | undefined;
909
- colors: Map<import("msa-parsers").Annotation, {
933
+ kind: "features";
934
+ legend: import("react-msaview").LegendEntry[];
935
+ colors: Map<import("react-msaview").Annotation, {
910
936
  fill: string;
911
937
  stroke: string;
912
938
  }>;
913
- legend: import("react-msaview").LegendEntry[];
939
+ legendKey?: string | undefined;
914
940
  legendTitle?: string | undefined;
915
- labels?: Map<import("msa-parsers").Annotation, string> | undefined;
941
+ labels?: Map<import("react-msaview").Annotation, string> | undefined;
916
942
  })[];
917
943
  readonly resolvedRowPanels: import("react-msaview").ResolvedRowPanel[];
918
944
  readonly featureAlignShifts: Map<string, Map<string, number>>;
@@ -922,6 +948,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
922
948
  } & {
923
949
  setHeaderHeight(arg: number): void;
924
950
  setHideHeader(arg: boolean): void;
951
+ setEmbeddedMode(arg: boolean): void;
925
952
  setImportForm(arg: boolean): void;
926
953
  treeOverviewClick(y: number): void;
927
954
  setTrackHeight(heightKey: string, height: number): void;
@@ -930,7 +957,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
930
957
  exportNewick(): void;
931
958
  setFilter(accession: string, shown: boolean): void;
932
959
  fit(): void;
933
- fitVertically(): void;
960
+ fitVertically(maxRowHeight?: any): void;
934
961
  zoomToRegion(region: import("react-msaview").Region): void;
935
962
  revealRegion(region: import("react-msaview").Region): void;
936
963
  zoomToSelection(): void;
@@ -941,7 +968,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
941
968
  col: number;
942
969
  row?: number;
943
970
  }): void;
944
- fitHorizontally(): void;
971
+ fitHorizontally(maxColWidth?: any): void;
945
972
  afterCreate(): void;
946
973
  } & {
947
974
  rid: string | undefined;
@@ -1143,7 +1170,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
1143
1170
  id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
1144
1171
  displayName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
1145
1172
  minimized: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
1146
- }, "id" | "type" | "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "treeAreaWidth" | "treeOrder" | "treeWidth" | "bgColor" | "colorSchemeName" | "customColorScheme" | "msaFormat" | "showColumnStats" | "allowedGappyness" | "clades" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "drawMsaLetters" | "encodings" | "features" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "msaFilehandle" | "region" | "relativeTo" | "residueMappings" | "rotated" | "rowHeight" | "rowPanels" | "scrollX" | "scrollY" | "scrollZoom" | "scrollZoomAxis" | "selection" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "trackHeights" | "treeFilehandle" | "treeMetadataFilehandle" | "treeRoot" | "turnedOffFeatures" | "turnedOffTracks"> & Omit<Omit<Omit<{}, "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "treeAreaWidth" | "treeOrder" | "treeWidth"> & {
1173
+ }, "id" | "type" | "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "showTreeScaleBar" | "treeAreaWidth" | "treeOrder" | "treeWidth" | "bgColor" | "colorSchemeName" | "customColorScheme" | "msaFormat" | "showColumnStats" | "allowedGappyness" | "clades" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "domainFill" | "drawMsaLetters" | "embeddedMode" | "encodings" | "features" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "msaFilehandle" | "region" | "relativeTo" | "residueMappings" | "rotated" | "rowHeight" | "rowPanels" | "scrollX" | "scrollY" | "scrollZoom" | "scrollZoomAxis" | "selection" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "trackHeights" | "treeFilehandle" | "treeMetadataFilehandle" | "treeRoot" | "turnedOffFeatures" | "turnedOffTracks"> & Omit<Omit<Omit<{}, "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "showTreeScaleBar" | "treeAreaWidth" | "treeOrder" | "treeWidth"> & {
1147
1174
  drawLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
1148
1175
  labelsAlignRight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
1149
1176
  treeAreaWidth: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
@@ -1154,22 +1181,25 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
1154
1181
  drawNodeBubbles: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
1155
1182
  drawNodeLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
1156
1183
  showTreeOverview: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
1184
+ showTreeScaleBar: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
1157
1185
  overviewHeight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
1158
1186
  }, "bgColor" | "colorSchemeName" | "customColorScheme" | "msaFormat" | "showColumnStats"> & {
1159
1187
  bgColor: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
1160
1188
  colorSchemeName: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
1161
1189
  customColorScheme: import("@jbrowse/mobx-state-tree").IType<Record<string, string> | undefined, Record<string, string> | undefined, Record<string, string> | undefined>;
1162
1190
  showColumnStats: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
1163
- msaFormat: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<import("msa-parsers").MSAFormat>>;
1164
- }, "id" | "type" | "allowedGappyness" | "clades" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "drawMsaLetters" | "encodings" | "features" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "msaFilehandle" | "region" | "relativeTo" | "residueMappings" | "rotated" | "rowHeight" | "rowPanels" | "scrollX" | "scrollY" | "scrollZoom" | "scrollZoomAxis" | "selection" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "trackHeights" | "treeFilehandle" | "treeMetadataFilehandle" | "treeRoot" | "turnedOffFeatures" | "turnedOffTracks"> & {
1191
+ msaFormat: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<import("react-msaview").MSAFormat>>;
1192
+ }, "id" | "type" | "allowedGappyness" | "clades" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "domainFill" | "drawMsaLetters" | "embeddedMode" | "encodings" | "features" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "msaFilehandle" | "region" | "relativeTo" | "residueMappings" | "rotated" | "rowHeight" | "rowPanels" | "scrollX" | "scrollY" | "scrollZoom" | "scrollZoomAxis" | "selection" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "trackHeights" | "treeFilehandle" | "treeMetadataFilehandle" | "treeRoot" | "turnedOffFeatures" | "turnedOffTracks"> & {
1165
1193
  id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
1166
1194
  showDomains: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
1195
+ domainFill: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
1167
1196
  showDomainLegend: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
1168
1197
  hideGaps: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
1169
1198
  allowedGappyness: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
1170
1199
  subFeatureRows: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
1171
1200
  type: import("@jbrowse/mobx-state-tree").ILiteralType<"MsaView">;
1172
1201
  drawMsaLetters: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
1202
+ embeddedMode: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
1173
1203
  scrollZoom: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
1174
1204
  scrollZoomAxis: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<"both" | "horizontal" | "vertical">, [undefined]>;
1175
1205
  height: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
@@ -1504,7 +1534,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
1504
1534
  showOnly: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
1505
1535
  turnedOffTracks: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>, [undefined]>;
1506
1536
  trackHeights: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<number>>, [undefined]>;
1507
- columnTracks: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("react-msaview").ColumnTrackSpec, import("react-msaview").ColumnTrackSpec, import("react-msaview").ColumnTrackSpec>>, [undefined]>;
1537
+ columnTracks: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").IType<import("react-msaview").ColumnTrackSpec, import("react-msaview").ColumnTrackSpec, import("react-msaview").ColumnTrackSpec>, import("react-msaview").ColumnTrackSpec, import("@jbrowse/mobx-state-tree")._NotCustomized>>, [undefined]>;
1508
1538
  residueMappings: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("react-msaview").ResidueMapping, import("react-msaview").ResidueMapping, import("react-msaview").ResidueMapping>>, [undefined]>;
1509
1539
  data: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IModelType<{
1510
1540
  tree: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
@@ -1527,9 +1557,9 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
1527
1557
  selection: import("@jbrowse/mobx-state-tree").IType<import("react-msaview").MsaSelection | undefined, import("react-msaview").MsaSelection | undefined, import("react-msaview").MsaSelection | undefined>;
1528
1558
  region: import("@jbrowse/mobx-state-tree").IType<import("react-msaview").Region | undefined, import("react-msaview").Region | undefined, import("react-msaview").Region | undefined>;
1529
1559
  clades: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("react-msaview").Clade, import("react-msaview").Clade, import("react-msaview").Clade>>, [undefined]>;
1530
- encodings: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("react-msaview").Encoding, import("react-msaview").Encoding, import("react-msaview").Encoding>>, [undefined]>;
1531
- rowPanels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("react-msaview").RowPanelSpec, import("react-msaview").RowPanelSpec, import("react-msaview").RowPanelSpec>>, [undefined]>;
1532
- }, "init" | "querySeqName" | "launchCompleted" | "embeddedMode" | "connectedViewId" | "connectedFeature" | "connectedTranscript" | "blastParams" | "orthologParams" | "querySeqOffset" | "uniprotId" | "zoomToBaseLevel" | "dataStoreId" | "mafRegion" | "domainsOnGenome"> & {
1560
+ encodings: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").IType<import("react-msaview").Encoding, import("react-msaview").Encoding, import("react-msaview").Encoding>, import("react-msaview").Encoding | import("react-msaview").LegacyEncoding, import("@jbrowse/mobx-state-tree")._NotCustomized>>, [undefined]>;
1561
+ rowPanels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").IType<import("react-msaview").RowPanelSpec, import("react-msaview").RowPanelSpec, import("react-msaview").RowPanelSpec>, import("react-msaview").LegacyRowPanel | import("react-msaview").RowPanelSpec, import("@jbrowse/mobx-state-tree")._NotCustomized>>, [undefined]>;
1562
+ }, "init" | "querySeqName" | "embeddedMode" | "launchCompleted" | "connectedViewId" | "connectedFeature" | "connectedTranscript" | "blastParams" | "orthologParams" | "querySeqOffset" | "uniprotId" | "zoomToBaseLevel" | "dataStoreId" | "mafRegion" | "domainsOnGenome"> & {
1533
1563
  connectedViewId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
1534
1564
  connectedFeature: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
1535
1565
  connectedTranscript: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
@@ -1545,12 +1575,12 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
1545
1575
  mafRegion: import("@jbrowse/mobx-state-tree").IType<MafRegion | undefined, MafRegion | undefined, MafRegion | undefined>;
1546
1576
  embeddedMode: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
1547
1577
  domainsOnGenome: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
1548
- }>, "id" | "type" | "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "treeAreaWidth" | "treeOrder" | "treeWidth" | "bgColor" | "colorSchemeName" | "customColorScheme" | "msaFormat" | "showColumnStats" | "allowedGappyness" | "clades" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "drawMsaLetters" | "encodings" | "features" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "msaFilehandle" | "region" | "relativeTo" | "residueMappings" | "rotated" | "rowHeight" | "rowPanels" | "scrollX" | "scrollY" | "scrollZoom" | "scrollZoomAxis" | "selection" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "trackHeights" | "treeFilehandle" | "treeMetadataFilehandle" | "treeRoot" | "turnedOffFeatures" | "turnedOffTracks"> & ({
1578
+ }>, "id" | "type" | "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "showTreeScaleBar" | "treeAreaWidth" | "treeOrder" | "treeWidth" | "bgColor" | "colorSchemeName" | "customColorScheme" | "msaFormat" | "showColumnStats" | "allowedGappyness" | "clades" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "domainFill" | "drawMsaLetters" | "embeddedMode" | "encodings" | "features" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "msaFilehandle" | "region" | "relativeTo" | "residueMappings" | "rotated" | "rowHeight" | "rowPanels" | "scrollX" | "scrollY" | "scrollZoom" | "scrollZoomAxis" | "selection" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "trackHeights" | "treeFilehandle" | "treeMetadataFilehandle" | "treeRoot" | "turnedOffFeatures" | "turnedOffTracks"> & ({
1549
1579
  bgColor: boolean;
1550
1580
  colorSchemeName: string;
1551
1581
  customColorScheme: Record<string, string> | undefined;
1552
1582
  showColumnStats: boolean;
1553
- msaFormat: import("msa-parsers").MSAFormat | undefined;
1583
+ msaFormat: import("react-msaview").MSAFormat | undefined;
1554
1584
  drawLabels: boolean;
1555
1585
  labelsAlignRight: boolean;
1556
1586
  treeAreaWidth: number | undefined;
@@ -1561,16 +1591,19 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
1561
1591
  drawNodeBubbles: boolean;
1562
1592
  drawNodeLabels: boolean;
1563
1593
  showTreeOverview: boolean;
1594
+ showTreeScaleBar: boolean;
1564
1595
  overviewHeight: number;
1565
1596
  columnTracks: import("react-msaview").ColumnTrackSpec[];
1566
1597
  id: string;
1567
1598
  showDomains: boolean;
1599
+ domainFill: boolean;
1568
1600
  showDomainLegend: boolean;
1569
1601
  hideGaps: boolean;
1570
1602
  allowedGappyness: number;
1571
1603
  subFeatureRows: boolean;
1572
1604
  type: "MsaView";
1573
1605
  drawMsaLetters: boolean;
1606
+ embeddedMode: boolean;
1574
1607
  scrollZoom: boolean;
1575
1608
  scrollZoomAxis: "both" | "horizontal" | "vertical";
1576
1609
  height: number;
@@ -1687,7 +1720,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
1687
1720
  colorSchemeName: string;
1688
1721
  customColorScheme: Record<string, string> | undefined;
1689
1722
  showColumnStats: boolean;
1690
- msaFormat: import("msa-parsers").MSAFormat | undefined;
1723
+ msaFormat: import("react-msaview").MSAFormat | undefined;
1691
1724
  drawLabels: boolean;
1692
1725
  labelsAlignRight: boolean;
1693
1726
  treeAreaWidth: number | undefined;
@@ -1698,16 +1731,19 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
1698
1731
  drawNodeBubbles: boolean;
1699
1732
  drawNodeLabels: boolean;
1700
1733
  showTreeOverview: boolean;
1734
+ showTreeScaleBar: boolean;
1701
1735
  overviewHeight: number;
1702
1736
  columnTracks?: undefined;
1703
1737
  id: string;
1704
1738
  showDomains: boolean;
1739
+ domainFill: boolean;
1705
1740
  showDomainLegend: boolean;
1706
1741
  hideGaps: boolean;
1707
1742
  allowedGappyness: number;
1708
1743
  subFeatureRows: boolean;
1709
1744
  type: "MsaView";
1710
1745
  drawMsaLetters: boolean;
1746
+ embeddedMode: boolean;
1711
1747
  scrollZoom: boolean;
1712
1748
  scrollZoomAxis: "both" | "horizontal" | "vertical";
1713
1749
  height: number;
@@ -1,2 +1,2 @@
1
- import{a as l}from"./chunk-XTQQNBQ5.js";import{a as i}from"./chunk-DNFD5II2.js";import{a as m}from"./chunk-BX4Z274Q.js";import{a}from"./chunk-J6KYLXRD.js";import{b as r}from"./chunk-FY3BTKY4.js";var e=r(a(),1),o=r(i(),1),t=r(m(),1);function c({onClose:n}){return e.default.createElement(o.Dialog,{open:!0,title:"About",onClose:()=>{n()}},e.default.createElement(t.DialogContent,null,e.default.createElement(t.Typography,null,"MSAView ",l," (",e.default.createElement(t.Link,{target:"_blank",rel:"noopener",href:"https://github.com/gmod/react-msaview"},"Github"),")"),e.default.createElement("ul",null,e.default.createElement("li",null,e.default.createElement(t.Typography,null,"We use some color schemes from the"," ",e.default.createElement(t.Link,{target:"_blank",rel:"noopener",href:"https://github.com/biotite-dev/biotite"},"biotite")," ","project, and their license is reproduced"," ",e.default.createElement(t.Link,{target:"_blank",rel:"noopener",href:"https://github.com/biotite-dev/biotite/blob/master/LICENSE.rst"},"here"))),e.default.createElement("li",null,e.default.createElement(t.Typography,null,"See this page for some information on jalview colorings"," ",e.default.createElement(t.Link,{target:"_blank",rel:"noopener",href:"https://www.jalview.org/help/html/colourSchemes/"},"here"))),e.default.createElement("li",null,e.default.createElement(t.Typography,null,"See this page for some info on the clustal, cinema, maeditor, and lesk color schemes"," ",e.default.createElement(t.Link,{target:"_blank",rel:"noopener",href:"http://www.bioinformatics.nl/~berndb/aacolour.html"},"here"))),e.default.createElement("li",null,e.default.createElement(t.Typography,null,"See this paper about the flower color scheme"," ",e.default.createElement(t.Link,{target:"_blank",rel:"noopener",href:"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7245768/"},"here"))))))}export{c as default};
2
- //# sourceMappingURL=AboutDialog-HCCCEJ6V.js.map
1
+ import{a as l}from"./chunk-WNIBTLFE.js";import{a as i}from"./chunk-DNFD5II2.js";import{a as m}from"./chunk-BX4Z274Q.js";import{a}from"./chunk-J6KYLXRD.js";import{b as r}from"./chunk-FY3BTKY4.js";var e=r(a(),1),o=r(i(),1),t=r(m(),1);function c({onClose:n}){return e.default.createElement(o.Dialog,{open:!0,title:"About",onClose:()=>{n()}},e.default.createElement(t.DialogContent,null,e.default.createElement(t.Typography,null,"MSAView ",l," (",e.default.createElement(t.Link,{target:"_blank",rel:"noopener",href:"https://github.com/gmod/react-msaview"},"Github"),")"),e.default.createElement("ul",null,e.default.createElement("li",null,e.default.createElement(t.Typography,null,"We use some color schemes from the"," ",e.default.createElement(t.Link,{target:"_blank",rel:"noopener",href:"https://github.com/biotite-dev/biotite"},"biotite")," ","project, and their license is reproduced"," ",e.default.createElement(t.Link,{target:"_blank",rel:"noopener",href:"https://github.com/biotite-dev/biotite/blob/master/LICENSE.rst"},"here"))),e.default.createElement("li",null,e.default.createElement(t.Typography,null,"See this page for some information on jalview colorings"," ",e.default.createElement(t.Link,{target:"_blank",rel:"noopener",href:"https://www.jalview.org/help/html/colourSchemes/"},"here"))),e.default.createElement("li",null,e.default.createElement(t.Typography,null,"See this page for some info on the clustal, cinema, maeditor, and lesk color schemes"," ",e.default.createElement(t.Link,{target:"_blank",rel:"noopener",href:"http://www.bioinformatics.nl/~berndb/aacolour.html"},"here"))),e.default.createElement("li",null,e.default.createElement(t.Typography,null,"See this paper about the flower color scheme"," ",e.default.createElement(t.Link,{target:"_blank",rel:"noopener",href:"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7245768/"},"here"))))))}export{c as default};
2
+ //# sourceMappingURL=AboutDialog-N23GOSSA.js.map
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "version": 3,
3
- "sources": ["../../node_modules/.pnpm/react-msaview@9.1.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/components/dialogs/AboutDialog.tsx"],
3
+ "sources": ["../../node_modules/.pnpm/react-msaview@9.4.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/components/dialogs/AboutDialog.tsx"],
4
4
  "sourcesContent": ["import React from 'react'\n\nimport { Dialog } from '@jbrowse/core/ui'\nimport { DialogContent, Link, Typography } from '@mui/material'\n\nimport { version } from '../../version.ts'\n\nexport default function AboutDialog({ onClose }: { onClose: () => void }) {\n return (\n <Dialog\n open\n title=\"About\"\n onClose={() => {\n onClose()\n }}\n >\n <DialogContent>\n <Typography>\n MSAView {version} (\n <Link\n target=\"_blank\"\n rel=\"noopener\"\n href=\"https://github.com/gmod/react-msaview\"\n >\n Github\n </Link>\n )\n </Typography>\n\n <ul>\n <li>\n <Typography>\n We use some color schemes from the{' '}\n <Link\n target=\"_blank\"\n rel=\"noopener\"\n href=\"https://github.com/biotite-dev/biotite\"\n >\n biotite\n </Link>{' '}\n project, and their license is reproduced{' '}\n <Link\n target=\"_blank\"\n rel=\"noopener\"\n href=\"https://github.com/biotite-dev/biotite/blob/master/LICENSE.rst\"\n >\n here\n </Link>\n </Typography>\n </li>\n <li>\n <Typography>\n See this page for some information on jalview colorings{' '}\n <Link\n target=\"_blank\"\n rel=\"noopener\"\n href=\"https://www.jalview.org/help/html/colourSchemes/\"\n >\n here\n </Link>\n </Typography>\n </li>\n <li>\n <Typography>\n See this page for some info on the clustal, cinema, maeditor, and\n lesk color schemes{' '}\n <Link\n target=\"_blank\"\n rel=\"noopener\"\n href=\"http://www.bioinformatics.nl/~berndb/aacolour.html\"\n >\n here\n </Link>\n </Typography>\n </li>\n <li>\n <Typography>\n See this paper about the flower color scheme{' '}\n <Link\n target=\"_blank\"\n rel=\"noopener\"\n href=\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7245768/\"\n >\n here\n </Link>\n </Typography>\n </li>\n </ul>\n </DialogContent>\n </Dialog>\n )\n}\n"],
5
5
  "mappings": "mMAAA,IAAAA,EAAkB,SAElBC,EAAuB,SACvBC,EAAgD,SAIlC,SAAPC,EAA6B,CAAE,QAAAC,CAAO,EAA2B,CACtE,OACE,EAAAC,QAAA,cAAC,SAAM,CACL,KAAI,GACJ,MAAM,QACN,QAAS,IAAK,CACZD,EAAO,CACT,CAAC,EAED,EAAAC,QAAA,cAAC,gBAAa,KACZ,EAAAA,QAAA,cAAC,aAAU,gBACAC,OACT,EAAAD,QAAA,cAAC,OAAI,CACH,OAAO,SACP,IAAI,WACJ,KAAK,uCAAuC,EAAA,QAAA,OAOhD,EAAAA,QAAA,cAAA,KAAA,KACE,EAAAA,QAAA,cAAA,KAAA,KACE,EAAAA,QAAA,cAAC,aAAU,0CAC0B,IACnC,EAAAA,QAAA,cAAC,OAAI,CACH,OAAO,SACP,IAAI,WACJ,KAAK,wCAAwC,EAAA,SAAA,EAGvC,+CACiC,IACzC,EAAAA,QAAA,cAAC,OAAI,CACH,OAAO,SACP,IAAI,WACJ,KAAK,gEAAgE,EAAA,MAAA,CAGhE,CACI,EAEf,EAAAA,QAAA,cAAA,KAAA,KACE,EAAAA,QAAA,cAAC,aAAU,+DAC+C,IACxD,EAAAA,QAAA,cAAC,OAAI,CACH,OAAO,SACP,IAAI,WACJ,KAAK,kDAAkD,EAAA,MAAA,CAGlD,CACI,EAEf,EAAAA,QAAA,cAAA,KAAA,KACE,EAAAA,QAAA,cAAC,aAAU,4FAEU,IACnB,EAAAA,QAAA,cAAC,OAAI,CACH,OAAO,SACP,IAAI,WACJ,KAAK,oDAAoD,EAAA,MAAA,CAGpD,CACI,EAEf,EAAAA,QAAA,cAAA,KAAA,KACE,EAAAA,QAAA,cAAC,aAAU,oDACoC,IAC7C,EAAAA,QAAA,cAAC,OAAI,CACH,OAAO,SACP,IAAI,WACJ,KAAK,uDAAuD,EAAA,MAAA,CAGvD,CACI,CACV,CACF,CACS,CAGtB",
6
6
  "names": ["import_react", "import_ui", "import_material", "AboutDialog", "onClose", "React", "version"]
@@ -0,0 +1,2 @@
1
+ import{g as d}from"./chunk-XZBGVA3Q.js";import"./chunk-K55ZVN73.js";import"./chunk-73KAPCJ2.js";import{a as x}from"./chunk-CVLB4VFP.js";import{a as C}from"./chunk-DNFD5II2.js";import{a as w}from"./chunk-BX4Z274Q.js";import{a as y}from"./chunk-J6KYLXRD.js";import{b as i}from"./chunk-FY3BTKY4.js";var e=i(y(),1),c=i(C(),1),t=i(w(),1),E=i(x(),1);var T="https://gmod.org/JBrowseMSA/tutorials/protein_family";async function b(l){let o=await fetch(l);if(!o.ok)throw new Error(`HTTP ${o.status} fetching ${l} ${await o.text()}`);return o.text()}var k=(0,E.observer)(function({handleClose:l,model:o}){let[r,h]=(0,e.useState)(),[a,g]=(0,e.useState)("file"),[s,F]=(0,e.useState)(""),[m,u]=(0,e.useState)(),[v,f]=(0,e.useState)(!1);return e.default.createElement(c.Dialog,{maxWidth:"xl",title:"Open annotation file",onClose:()=>{l()},open:!0},e.default.createElement(t.DialogContent,null,m?e.default.createElement(c.ErrorMessage,{error:m}):null,e.default.createElement(t.Typography,null,"Open a GFF3 file of annotations, such as the one `react-msaview-cli interpro` writes, or the JSON an InterProScan run returns."," ",e.default.createElement(t.Link,{href:T,target:"_blank",rel:"noopener noreferrer"},"How to make one")),e.default.createElement("div",{style:{display:"flex",margin:30}},e.default.createElement(t.FormControl,{component:"fieldset"},e.default.createElement(t.RadioGroup,{value:a,onChange:n=>{g(n.target.value)}},e.default.createElement(t.FormControlLabel,{value:"url",control:e.default.createElement(t.Radio,null),label:"URL"}),e.default.createElement(t.FormControlLabel,{value:"file",control:e.default.createElement(t.Radio,null),label:"File"}))),a==="url"?e.default.createElement("div",null,e.default.createElement(t.Typography,null,"Open an annotation file from a URL"),e.default.createElement(t.TextField,{label:"URL",value:s,onChange:n=>{F(n.target.value)}})):e.default.createElement("div",{style:{paddingTop:20}},e.default.createElement(t.Typography,null,"Open an annotation file from your local drive"),e.default.createElement(t.Button,{variant:"outlined",component:"label"},"Choose File",e.default.createElement("input",{type:"file",hidden:!0,onChange:({target:n})=>{let p=n.files?.[0];p&&h(p)}})),r?e.default.createElement(t.Typography,null,r.name):null))),e.default.createElement(t.DialogActions,null,e.default.createElement(t.Button,{variant:"contained",color:"primary",disabled:v||(a==="file"?!r:!s.trim()),onClick:()=>{(async()=>{f(!0),u(void 0);try{let n=await(a==="file"&&r?r.text():b(s));o.setGFFFilehandle(void 0),o.setGFF(d(n)),o.setShowDomains(!0),o.setCellFill("domain"),l()}catch(n){console.error(n),u(n)}finally{f(!1)}})()}},"Open annotations"),e.default.createElement(t.Button,{variant:"contained",color:"secondary",onClick:()=>{l()}},"Cancel")))}),O=k;export{O as default};
2
+ //# sourceMappingURL=AnnotationFileDialog-FVQNLVEU.js.map
@@ -0,0 +1,7 @@
1
+ {
2
+ "version": 3,
3
+ "sources": ["../../node_modules/.pnpm/react-msaview@9.4.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/components/dialogs/AnnotationFileDialog.tsx"],
4
+ "sourcesContent": ["import React, { useState } from 'react'\n\nimport { Dialog, ErrorMessage } from '@jbrowse/core/ui'\nimport {\n Button,\n DialogActions,\n DialogContent,\n FormControl,\n FormControlLabel,\n Link,\n Radio,\n RadioGroup,\n TextField,\n Typography,\n} from '@mui/material'\nimport { observer } from 'mobx-react'\nimport { annotationTextToGFF } from 'msa-parsers'\n\nimport type { MsaViewModel } from '../../model.ts'\n\nconst domainsTutorial = 'https://gmod.org/JBrowseMSA/tutorials/protein_family'\n\nasync function fetchText(url: string) {\n const response = await fetch(url)\n if (!response.ok) {\n throw new Error(\n `HTTP ${response.status} fetching ${url} ${await response.text()}`,\n )\n }\n return response.text()\n}\n\nconst AnnotationFileDialog = observer(function ({\n handleClose,\n model,\n}: {\n handleClose: () => void\n model: MsaViewModel\n}) {\n const [file, setFile] = useState<File>()\n const [choice, setChoice] = useState('file')\n const [url, setUrl] = useState('')\n const [error, setError] = useState<unknown>()\n const [loading, setLoading] = useState(false)\n\n // the error is shown here rather than notified: the standalone app and the\n // MSAViewer component have no jbrowse session to notify, and asking one for\n // its notify() threw out of the success path into the catch, which threw\n // again on the same missing session\n return (\n <Dialog\n maxWidth=\"xl\"\n title=\"Open annotation file\"\n onClose={() => {\n handleClose()\n }}\n open\n >\n <DialogContent>\n {error ? <ErrorMessage error={error} /> : null}\n <Typography>\n Open a GFF3 file of annotations, such as the one `react-msaview-cli\n interpro` writes, or the JSON an InterProScan run returns.{' '}\n <Link\n href={domainsTutorial}\n target=\"_blank\"\n rel=\"noopener noreferrer\"\n >\n How to make one\n </Link>\n </Typography>\n\n <div style={{ display: 'flex', margin: 30 }}>\n <FormControl component=\"fieldset\">\n <RadioGroup\n value={choice}\n onChange={event => {\n setChoice(event.target.value)\n }}\n >\n <FormControlLabel value=\"url\" control={<Radio />} label=\"URL\" />\n <FormControlLabel value=\"file\" control={<Radio />} label=\"File\" />\n </RadioGroup>\n </FormControl>\n {choice === 'url' ? (\n <div>\n <Typography>Open an annotation file from a URL</Typography>\n <TextField\n label=\"URL\"\n value={url}\n onChange={event => {\n setUrl(event.target.value)\n }}\n />\n </div>\n ) : (\n <div style={{ paddingTop: 20 }}>\n <Typography>\n Open an annotation file from your local drive\n </Typography>\n <Button variant=\"outlined\" component=\"label\">\n Choose File\n <input\n type=\"file\"\n hidden\n onChange={({ target }) => {\n const chosen = target.files?.[0]\n if (chosen) {\n setFile(chosen)\n }\n }}\n />\n </Button>\n {file ? <Typography>{file.name}</Typography> : null}\n </div>\n )}\n </div>\n </DialogContent>\n <DialogActions>\n <Button\n variant=\"contained\"\n color=\"primary\"\n disabled={loading || (choice === 'file' ? !file : !url.trim())}\n onClick={() => {\n // eslint-disable-next-line @typescript-eslint/no-floating-promises\n ;(async () => {\n setLoading(true)\n setError(undefined)\n try {\n const text = await (choice === 'file' && file\n ? file.text()\n : fetchText(url))\n // through the model's own GFF text, so the annotations travel\n // in the snapshot and the shared URL like every other layer. A\n // filehandle left set would make the snapshot drop that text\n model.setGFFFilehandle(undefined)\n model.setGFF(annotationTextToGFF(text))\n model.setShowDomains(true)\n model.setCellFill('domain')\n handleClose()\n } catch (e) {\n console.error(e)\n setError(e)\n } finally {\n setLoading(false)\n }\n })()\n }}\n >\n Open annotations\n </Button>\n <Button\n variant=\"contained\"\n color=\"secondary\"\n onClick={() => {\n handleClose()\n }}\n >\n Cancel\n </Button>\n </DialogActions>\n </Dialog>\n )\n})\n\nexport default AnnotationFileDialog\n"],
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6
+ "names": ["import_react", "import_ui", "import_material", "import_mobx_react", "domainsTutorial", "fetchText", "url", "response", "AnnotationFileDialog", "handleClose", "model", "file", "setFile", "choice", "setChoice", "setUrl", "error", "setError", "loading", "setLoading", "React", "event", "target", "chosen", "text", "annotationTextToGFF", "e", "AnnotationFileDialog_default"]
7
+ }
@@ -1,2 +1,2 @@
1
- import{a as p}from"./chunk-GAY2PLS6.js";import{X as v,Y as y}from"./chunk-ZQSWX57C.js";import{a as L}from"./chunk-CVLB4VFP.js";import{a as D}from"./chunk-DNFD5II2.js";import{a as V}from"./chunk-BX4Z274Q.js";import{a as I}from"./chunk-J6KYLXRD.js";import{b as l}from"./chunk-FY3BTKY4.js";var t=l(I(),1),i=l(D(),1),e=l(V(),1),k=l(L(),1);function z(r){requestAnimationFrame(()=>{requestAnimationFrame(r)})}var P=(0,k.observer)(function({model:r,onClose:c}){let[s,C]=(0,t.useState)(!0),[n,T]=(0,t.useState)(!0),[o,b]=(0,t.useState)("viewport"),[E,w]=(0,t.useState)(),[m,h]=(0,t.useState)(!1),d=(0,e.useTheme)(),{turnedOnTracks:M,numColumns:S,leaves:A,showMsaLetters:F}=r,g=M.length>0,x=y(r,v(r,{theme:d,exportType:"entire",includeTracks:n})),f=F&&o==="entire"?S*A.length:0,G=f>1e5;return t.default.createElement(i.Dialog,{onClose:()=>{c()},open:!0,title:"Export SVG"},t.default.createElement(e.DialogContent,null,E?t.default.createElement(i.ErrorMessage,{error:E}):null,t.default.createElement(e.Typography,null,"Settings:"),t.default.createElement(p,{label:"Include minimap?",disabled:o==="entire",checked:s,onChange:()=>{C(!s)}}),g?t.default.createElement(p,{label:"Include tracks?",checked:n,onChange:()=>{T(!n)}}):null,t.default.createElement("div",null,t.default.createElement(e.FormControl,null,t.default.createElement(e.FormLabel,null,"Export type"),t.default.createElement(e.RadioGroup,{value:o,onChange:a=>{let{value:u}=a.target;(u==="entire"||u==="viewport")&&b(u)}},t.default.createElement(e.FormControlLabel,{value:"entire",control:t.default.createElement(e.Radio,null),label:"Entire MSA"}),t.default.createElement(e.FormControlLabel,{value:"viewport",control:t.default.createElement(e.Radio,null),label:"Current viewport only"})))),G?t.default.createElement(e.Alert,{severity:"warning",style:{marginTop:8}},"The entire MSA is ",Math.round(x.width),"x",Math.round(x.height)," pixels and draws"," ",Math.round(f/1e3),"k residue letters, each its own SVG element. Export may be slow or fail \u2014 zooming out far enough to hide the letters exports the same alignment as an image instead."):null),t.default.createElement(e.DialogActions,null,t.default.createElement(e.Button,{variant:"contained",color:"primary",disabled:m,startIcon:m?t.default.createElement(e.CircularProgress,{size:16,color:"inherit"}):null,onClick:()=>{h(!0),z(()=>{r.exportSVG({theme:d,includeMinimap:s,includeTracks:g&&n,exportType:o}).then(()=>{c()}).catch(a=>{console.error(a),w(a)}).finally(()=>{h(!1)})})}},m?"Exporting\u2026":"Export"),t.default.createElement(e.Button,{variant:"contained",color:"secondary",onClick:()=>{c()}},"Cancel")))}),B=P;export{B as default};
2
- //# sourceMappingURL=ExportSVGDialog-YUFLYBYW.js.map
1
+ import{a as p}from"./chunk-RFKEQQMZ.js";import{$ as y,_ as v}from"./chunk-SYZYE3AS.js";import{a as L}from"./chunk-CVLB4VFP.js";import{a as D}from"./chunk-DNFD5II2.js";import{a as V}from"./chunk-BX4Z274Q.js";import{a as I}from"./chunk-J6KYLXRD.js";import{b as l}from"./chunk-FY3BTKY4.js";var t=l(I(),1),i=l(D(),1),e=l(V(),1),k=l(L(),1);function z(r){requestAnimationFrame(()=>{requestAnimationFrame(r)})}var P=(0,k.observer)(function({model:r,onClose:c}){let[s,C]=(0,t.useState)(!0),[n,T]=(0,t.useState)(!0),[o,b]=(0,t.useState)("viewport"),[E,w]=(0,t.useState)(),[m,h]=(0,t.useState)(!1),d=(0,e.useTheme)(),{turnedOnTracks:M,numColumns:S,leaves:A,showMsaLetters:F}=r,g=M.length>0,x=y(r,v(r,{theme:d,exportType:"entire",includeTracks:n})),f=F&&o==="entire"?S*A.length:0,G=f>1e5;return t.default.createElement(i.Dialog,{onClose:()=>{c()},open:!0,title:"Export SVG"},t.default.createElement(e.DialogContent,null,E?t.default.createElement(i.ErrorMessage,{error:E}):null,t.default.createElement(e.Typography,null,"Settings:"),t.default.createElement(p,{label:"Include minimap?",disabled:o==="entire",checked:s,onChange:()=>{C(!s)}}),g?t.default.createElement(p,{label:"Include tracks?",checked:n,onChange:()=>{T(!n)}}):null,t.default.createElement("div",null,t.default.createElement(e.FormControl,null,t.default.createElement(e.FormLabel,null,"Export type"),t.default.createElement(e.RadioGroup,{value:o,onChange:a=>{let{value:u}=a.target;(u==="entire"||u==="viewport")&&b(u)}},t.default.createElement(e.FormControlLabel,{value:"entire",control:t.default.createElement(e.Radio,null),label:"Entire MSA"}),t.default.createElement(e.FormControlLabel,{value:"viewport",control:t.default.createElement(e.Radio,null),label:"Current viewport only"})))),G?t.default.createElement(e.Alert,{severity:"warning",style:{marginTop:8}},"The entire MSA is ",Math.round(x.width),"x",Math.round(x.height)," pixels and draws"," ",Math.round(f/1e3),"k residue letters, each its own SVG element. Export may be slow or fail \u2014 zooming out far enough to hide the letters exports the same alignment as an image instead."):null),t.default.createElement(e.DialogActions,null,t.default.createElement(e.Button,{variant:"contained",color:"primary",disabled:m,startIcon:m?t.default.createElement(e.CircularProgress,{size:16,color:"inherit"}):null,onClick:()=>{h(!0),z(()=>{r.exportSVG({theme:d,includeMinimap:s,includeTracks:g&&n,exportType:o}).then(()=>{c()}).catch(a=>{console.error(a),w(a)}).finally(()=>{h(!1)})})}},m?"Exporting\u2026":"Export"),t.default.createElement(e.Button,{variant:"contained",color:"secondary",onClick:()=>{c()}},"Cancel")))}),B=P;export{B as default};
2
+ //# sourceMappingURL=ExportSVGDialog-3SA6HFZB.js.map
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "version": 3,
3
- "sources": ["../../node_modules/.pnpm/react-msaview@9.1.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/components/dialogs/ExportSVGDialog.tsx"],
3
+ "sources": ["../../node_modules/.pnpm/react-msaview@9.4.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/components/dialogs/ExportSVGDialog.tsx"],
4
4
  "sourcesContent": ["import React, { useState } from 'react'\n\nimport { Dialog, ErrorMessage } from '@jbrowse/core/ui'\nimport {\n Alert,\n Button,\n CircularProgress,\n DialogActions,\n DialogContent,\n FormControl,\n FormControlLabel,\n FormLabel,\n Radio,\n RadioGroup,\n Typography,\n useTheme,\n} from '@mui/material'\nimport { observer } from 'mobx-react'\n\nimport { exportPageSize, getLayout } from '../../exportLayout.ts'\nimport Checkbox2 from '../Checkbox2.tsx'\n\nimport type { MsaViewModel } from '../../model.ts'\n\n// Run after the browser has painted. A requestAnimationFrame callback still\n// runs *before* the frame it was queued for, so one alone hands the main thread\n// to the render with the spinner not yet on screen; the second fires once that\n// frame is out.\nfunction afterPaint(fn: () => void) {\n requestAnimationFrame(() => {\n requestAnimationFrame(fn)\n })\n}\n\nconst ExportSVGDialog = observer(function ({\n model,\n onClose,\n}: {\n model: MsaViewModel\n onClose: () => void\n}) {\n const [includeMinimap, setIncludeMinimap] = useState(true)\n const [includeTracks, setIncludeTracks] = useState(true)\n const [exportType, setExportType] = useState<'entire' | 'viewport'>(\n 'viewport',\n )\n const [error, setError] = useState<unknown>()\n const [exporting, setExporting] = useState(false)\n const theme = useTheme()\n const { turnedOnTracks, numColumns, leaves, showMsaLetters } = model\n const hasTracks = turnedOnTracks.length > 0\n const entire = exportPageSize(\n model,\n getLayout(model, { theme, exportType: 'entire', includeTracks }),\n )\n // the background is one raster image whatever its size, so what the figure\n // actually costs is its residue letters: each is an svg element of its own.\n // Past roughly this many the export runs to tens of seconds and can exhaust\n // the tab's memory outright\n const glyphs =\n showMsaLetters && exportType === 'entire' ? numColumns * leaves.length : 0\n const isLargeExport = glyphs > 100_000\n return (\n <Dialog\n onClose={() => {\n onClose()\n }}\n open\n title=\"Export SVG\"\n >\n <DialogContent>\n {error ? <ErrorMessage error={error} /> : null}\n <Typography>Settings:</Typography>\n <Checkbox2\n label=\"Include minimap?\"\n disabled={exportType === 'entire'}\n checked={includeMinimap}\n onChange={() => {\n setIncludeMinimap(!includeMinimap)\n }}\n />\n {hasTracks ? (\n <Checkbox2\n label=\"Include tracks?\"\n checked={includeTracks}\n onChange={() => {\n setIncludeTracks(!includeTracks)\n }}\n />\n ) : null}\n <div>\n <FormControl>\n <FormLabel>Export type</FormLabel>\n <RadioGroup\n value={exportType}\n onChange={event => {\n const { value } = event.target\n if (value === 'entire' || value === 'viewport') {\n setExportType(value)\n }\n }}\n >\n <FormControlLabel\n value=\"entire\"\n control={<Radio />}\n label=\"Entire MSA\"\n />\n <FormControlLabel\n value=\"viewport\"\n control={<Radio />}\n label=\"Current viewport only\"\n />\n </RadioGroup>\n </FormControl>\n </div>\n {isLargeExport ? (\n <Alert severity=\"warning\" style={{ marginTop: 8 }}>\n The entire MSA is {Math.round(entire.width)}x\n {Math.round(entire.height)} pixels and draws{' '}\n {Math.round(glyphs / 1000)}k residue letters, each its own SVG\n element. Export may be slow or fail \u2014 zooming out far enough to hide\n the letters exports the same alignment as an image instead.\n </Alert>\n ) : null}\n </DialogContent>\n <DialogActions>\n <Button\n variant=\"contained\"\n color=\"primary\"\n // rendering runs on the main thread and a large figure holds it for\n // seconds; without this the button stays live through the freeze and\n // a second click starts a second export\n disabled={exporting}\n startIcon={\n exporting ? <CircularProgress size={16} color=\"inherit\" /> : null\n }\n onClick={() => {\n setExporting(true)\n afterPaint(() => {\n void model\n .exportSVG({\n theme,\n includeMinimap,\n includeTracks: hasTracks && includeTracks,\n exportType,\n })\n .then(() => {\n onClose()\n })\n .catch((e: unknown) => {\n console.error(e)\n setError(e)\n })\n .finally(() => {\n setExporting(false)\n })\n })\n }}\n >\n {exporting ? 'Exporting\u2026' : 'Export'}\n </Button>\n <Button\n variant=\"contained\"\n color=\"secondary\"\n onClick={() => {\n onClose()\n }}\n >\n Cancel\n </Button>\n </DialogActions>\n </Dialog>\n )\n})\n\nexport default ExportSVGDialog\n"],
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