jbrowse-plugin-msaview 5.3.0 → 5.4.0

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Files changed (86) hide show
  1. package/dist/MsaViewPanel/model.d.ts +24 -22
  2. package/dist/MsaViewPanel/model.js +7 -0
  3. package/dist/MsaViewPanel/model.test.js +3 -0
  4. package/dist/chunks/{AboutDialog-447TIFAW.js → AboutDialog-HCCCEJ6V.js} +2 -2
  5. package/dist/chunks/{AboutDialog-447TIFAW.js.map → AboutDialog-HCCCEJ6V.js.map} +1 -1
  6. package/dist/chunks/AnnotationFileDialog-CPJ4X7XW.js +2 -0
  7. package/dist/chunks/{AnnotationFileDialog-S3N5EHHE.js.map → AnnotationFileDialog-CPJ4X7XW.js.map} +2 -2
  8. package/dist/chunks/{ExportSVGDialog-7ZHKKQ7W.js → ExportSVGDialog-YUFLYBYW.js} +2 -2
  9. package/dist/chunks/{ExportSVGDialog-7ZHKKQ7W.js.map → ExportSVGDialog-YUFLYBYW.js.map} +1 -1
  10. package/dist/chunks/{FeatureDialog-EEOGSLOG.js → FeatureDialog-NBDB5SWU.js} +1 -1
  11. package/dist/chunks/{FeatureDialog-EEOGSLOG.js.map → FeatureDialog-NBDB5SWU.js.map} +1 -1
  12. package/dist/chunks/{HelpDialog-TCWNBZOV.js → HelpDialog-UCUYPCOI.js} +2 -2
  13. package/dist/chunks/{HelpDialog-TCWNBZOV.js.map → HelpDialog-UCUYPCOI.js.map} +1 -1
  14. package/dist/chunks/{LaunchMsaViewDialog-R6CNRASN.js → LaunchMsaViewDialog-HGL6P4E4.js} +2 -2
  15. package/dist/chunks/{LaunchMsaViewDialog-R6CNRASN.js.map → LaunchMsaViewDialog-HGL6P4E4.js.map} +2 -2
  16. package/dist/chunks/MetadataDialog-DSA3545E.js +2 -0
  17. package/dist/chunks/{MetadataDialog-MNSI6NEW.js.map → MetadataDialog-DSA3545E.js.map} +2 -2
  18. package/dist/chunks/MsaViewPanel-XSXFJWWY.js +2 -0
  19. package/dist/chunks/{MsaViewPanel-R2WAER5O.js.map → MsaViewPanel-XSXFJWWY.js.map} +1 -1
  20. package/dist/chunks/{TrackInfoDialog-W2F77IPG.js → TrackInfoDialog-YXCIGFYM.js} +2 -2
  21. package/dist/chunks/{TrackInfoDialog-W2F77IPG.js.map → TrackInfoDialog-YXCIGFYM.js.map} +1 -1
  22. package/dist/chunks/TreeNodeInfoDialog-QCWDJTM4.js +2 -0
  23. package/dist/chunks/{TreeNodeInfoDialog-T5XMPG3R.js.map → TreeNodeInfoDialog-QCWDJTM4.js.map} +2 -2
  24. package/dist/chunks/{chunk-BAM67QHH.js → chunk-2XCUSA22.js} +2 -2
  25. package/dist/chunks/{chunk-JF6CW6MO.js → chunk-35FWLG3N.js} +1 -1
  26. package/dist/chunks/{chunk-JF6CW6MO.js.map → chunk-35FWLG3N.js.map} +1 -1
  27. package/dist/chunks/{chunk-NWHZOZMG.js → chunk-5OSSOQH4.js} +1 -1
  28. package/dist/chunks/{chunk-NWHZOZMG.js.map → chunk-5OSSOQH4.js.map} +1 -1
  29. package/dist/chunks/{chunk-FEUZKN5V.js → chunk-666BV764.js} +2 -2
  30. package/dist/chunks/{chunk-FEUZKN5V.js.map → chunk-666BV764.js.map} +1 -1
  31. package/dist/chunks/{chunk-YUKJI2AH.js → chunk-AQ2THRTR.js} +2 -2
  32. package/dist/chunks/{chunk-YUKJI2AH.js.map → chunk-AQ2THRTR.js.map} +1 -1
  33. package/dist/chunks/{chunk-L6CBIH6H.js → chunk-ASUKJX5J.js} +2 -2
  34. package/dist/chunks/{chunk-L6CBIH6H.js.map → chunk-ASUKJX5J.js.map} +1 -1
  35. package/dist/chunks/chunk-F726IWCW.js +2 -0
  36. package/dist/chunks/chunk-F726IWCW.js.map +7 -0
  37. package/dist/chunks/{chunk-CSCUNTGJ.js → chunk-FFHB7WP7.js} +4 -4
  38. package/dist/chunks/chunk-FFHB7WP7.js.map +7 -0
  39. package/dist/chunks/{chunk-ERCMNTEQ.js → chunk-GAY2PLS6.js} +1 -1
  40. package/dist/chunks/{chunk-ERCMNTEQ.js.map → chunk-GAY2PLS6.js.map} +1 -1
  41. package/dist/chunks/{chunk-TSHN6J7U.js → chunk-JDQUBCHM.js} +1 -1
  42. package/dist/chunks/{chunk-TSHN6J7U.js.map → chunk-JDQUBCHM.js.map} +1 -1
  43. package/dist/chunks/{chunk-IBBQUV2I.js → chunk-KSCGTF4R.js} +1 -1
  44. package/dist/chunks/{chunk-IBBQUV2I.js.map → chunk-KSCGTF4R.js.map} +1 -1
  45. package/dist/chunks/{chunk-6YFCSBEE.js → chunk-NLAW2OYS.js} +2 -2
  46. package/dist/chunks/{chunk-6YFCSBEE.js.map → chunk-NLAW2OYS.js.map} +1 -1
  47. package/dist/chunks/chunk-QQKPT6EL.js +2 -0
  48. package/dist/chunks/{chunk-XVNCZQMR.js.map → chunk-QQKPT6EL.js.map} +1 -1
  49. package/dist/chunks/{chunk-WAPIOD25.js → chunk-WMDOEOAH.js} +5 -5
  50. package/dist/chunks/{chunk-WAPIOD25.js.map → chunk-WMDOEOAH.js.map} +1 -1
  51. package/dist/chunks/chunk-XTQQNBQ5.js +2 -0
  52. package/dist/chunks/{chunk-6EOYBBT4.js.map → chunk-XTQQNBQ5.js.map} +1 -1
  53. package/dist/chunks/chunk-XXCNVFGP.js +11 -0
  54. package/dist/chunks/chunk-XXCNVFGP.js.map +7 -0
  55. package/dist/chunks/{chunk-OVAXNTPN.js → chunk-ZQSWX57C.js} +1 -1
  56. package/dist/chunks/{chunk-OVAXNTPN.js.map → chunk-ZQSWX57C.js.map} +1 -1
  57. package/dist/chunks/dist-GZKCGB2N.js +2 -0
  58. package/dist/chunks/{model-TCPB6WNJ.js → model-36HCIOZJ.js} +3 -3
  59. package/dist/chunks/model-36HCIOZJ.js.map +7 -0
  60. package/dist/chunks/{renderToSvg-53FEV6IJ.js → renderToSvg-5DMIQ72S.js} +2 -2
  61. package/dist/jbrowse-plugin-msaview.esm.js +2 -2
  62. package/dist/jbrowse-plugin-msaview.esm.js.map +2 -2
  63. package/dist/version.d.ts +1 -1
  64. package/dist/version.js +1 -1
  65. package/package.json +17 -17
  66. package/src/MsaViewPanel/model.test.ts +4 -0
  67. package/src/MsaViewPanel/model.ts +8 -0
  68. package/src/version.ts +1 -1
  69. package/dist/chunks/AnnotationFileDialog-S3N5EHHE.js +0 -2
  70. package/dist/chunks/MetadataDialog-MNSI6NEW.js +0 -2
  71. package/dist/chunks/MsaViewPanel-R2WAER5O.js +0 -2
  72. package/dist/chunks/TreeNodeInfoDialog-T5XMPG3R.js +0 -2
  73. package/dist/chunks/chunk-6EOYBBT4.js +0 -2
  74. package/dist/chunks/chunk-A63PUWQZ.js +0 -6
  75. package/dist/chunks/chunk-A63PUWQZ.js.map +0 -7
  76. package/dist/chunks/chunk-CSCUNTGJ.js.map +0 -7
  77. package/dist/chunks/chunk-DEFUNIWW.js +0 -8
  78. package/dist/chunks/chunk-DEFUNIWW.js.map +0 -7
  79. package/dist/chunks/chunk-K55ZVN73.js +0 -5
  80. package/dist/chunks/chunk-K55ZVN73.js.map +0 -7
  81. package/dist/chunks/chunk-XVNCZQMR.js +0 -2
  82. package/dist/chunks/dist-N4ZJK63Q.js +0 -2
  83. package/dist/chunks/model-TCPB6WNJ.js.map +0 -7
  84. /package/dist/chunks/{chunk-BAM67QHH.js.map → chunk-2XCUSA22.js.map} +0 -0
  85. /package/dist/chunks/{dist-N4ZJK63Q.js.map → dist-GZKCGB2N.js.map} +0 -0
  86. /package/dist/chunks/{renderToSvg-53FEV6IJ.js.map → renderToSvg-5DMIQ72S.js.map} +0 -0
@@ -128,7 +128,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
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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("react-msaview").MSAFormat>>;
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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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  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]>;
@@ -497,7 +497,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
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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" | "connectedViewId" | "connectedFeature" | "connectedTranscript" | "blastParams" | "orthologParams" | "querySeqOffset" | "uniprotId" | "zoomToBaseLevel" | "dataStoreId" | "mafRegion"> & {
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+ }, "init" | "querySeqName" | "launchCompleted" | "embeddedMode" | "connectedViewId" | "connectedFeature" | "connectedTranscript" | "blastParams" | "orthologParams" | "querySeqOffset" | "uniprotId" | "zoomToBaseLevel" | "dataStoreId" | "mafRegion"> & {
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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>>;
@@ -511,6 +511,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
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  dataStoreId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
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  launchCompleted: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
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  mafRegion: import("@jbrowse/mobx-state-tree").IType<MafRegion | undefined, MafRegion | undefined, MafRegion | undefined>;
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+ embeddedMode: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
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  }, {
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  width: number;
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  bodyMounted: boolean;
@@ -549,7 +550,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
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  setCustomColorScheme(map?: Record<string, string>): void;
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  setBgColor(arg: boolean): void;
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  setShowColumnStats(arg: boolean): void;
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- setMSAFormat(arg?: import("react-msaview").MSAFormat): void;
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+ setMSAFormat(arg?: import("msa-parsers").MSAFormat): void;
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  } & {
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  headerHeight: number;
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  hideHeader: boolean;
@@ -581,7 +582,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
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  dismissedWarnings: string[];
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  resetCount: number;
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  hostCarriesData: boolean;
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- annotations: import("react-msaview").Annotation[];
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+ annotations: import("msa-parsers").Annotation[];
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  } & {
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  drawRelativeTo(id: string | undefined): void;
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  setHideGaps(arg: boolean): void;
@@ -632,7 +633,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
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  setGFF(result?: string): void;
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  } & {
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  readonly hideGapsEffective: boolean;
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- readonly allAnnotations: import("react-msaview").Annotation[];
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+ readonly allAnnotations: import("msa-parsers").Annotation[];
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  readonly actuallyShowDomains: boolean;
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  readonly hostRestoresData: boolean;
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  readonly viewInitialized: boolean;
@@ -660,7 +661,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
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  readonly rowData: Record<string, Record<string, string> | undefined>;
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  rowDataOf(name: string): Record<string, string> | undefined;
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  readonly rowFields: string[];
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- readonly MSA: import("react-msaview").MSAParserType | null;
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+ readonly MSA: import("msa-parsers").MSAParserType | null;
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  readonly numColumns: number;
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  readonly inputTree: import("react-msaview").NodeWithIds;
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  readonly tree: import("react-msaview").NodeWithIds;
@@ -791,9 +792,9 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
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  readonly topBandHeight: number;
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  readonly msaAreaHeight: number;
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  readonly totalTrackAreaHeight: number;
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- readonly annotationTypes: Map<string, import("react-msaview").Annotation>;
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- readonly filteredAnnotations: import("react-msaview").Annotation[];
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- readonly annotationsByRow: Record<string, import("react-msaview").Annotation[]>;
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+ readonly annotationTypes: Map<string, import("msa-parsers").Annotation>;
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+ readonly filteredAnnotations: import("msa-parsers").Annotation[];
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+ readonly annotationsByRow: Record<string, import("msa-parsers").Annotation[]>;
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  } & {
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  readonly showVerticalScrollbar: boolean;
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  } & {
@@ -826,7 +827,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
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  zoomToPos(scaleFactor: number, offsetX: number, offsetY: number, axis?: "both" | "horizontal" | "vertical"): void;
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  doScrollY(deltaY: number): void;
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  setScrollY(n: number): void;
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- setAnnotations(annotations: import("react-msaview").Annotation[]): void;
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+ setAnnotations(annotations: import("msa-parsers").Annotation[]): void;
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  applyGFFText(gffText: string): void;
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  doScrollX(deltaX: number): void;
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  setScrollX(n: number): void;
@@ -845,24 +846,24 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
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  readonly hoveredCell: import("react-msaview").Cell | undefined;
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  readonly clickedCell: import("react-msaview").Cell | undefined;
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  readonly viewport: import("react-msaview").Viewport | undefined;
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- readonly segmentDomainTypes: import("react-msaview").Annotation[];
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- readonly categoricalDomainTypes: import("react-msaview").Annotation[];
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+ readonly segmentDomainTypes: import("msa-parsers").Annotation[];
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+ readonly categoricalDomainTypes: import("msa-parsers").Annotation[];
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  readonly fillPalette: {
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  [x: string]: string;
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  };
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  readonly featureFillEncoding: import("react-msaview").ResolvedEncoding | undefined;
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- readonly featureColors: Map<import("react-msaview").Annotation, {
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+ readonly featureColors: Map<import("msa-parsers").Annotation, {
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  fill: string;
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  stroke: string;
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  }>;
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- readonly featureLabels: Map<import("react-msaview").Annotation, string> | undefined;
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+ readonly featureLabels: Map<import("msa-parsers").Annotation, string> | undefined;
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  readonly segmentLabels: Map<string, string>;
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- readonly visibleDomainTypes: import("react-msaview").Annotation[];
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+ readonly visibleDomainTypes: import("msa-parsers").Annotation[];
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  readonly legends: import("react-msaview").Legend[];
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  readonly domainUnderline: boolean;
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  readonly domainBands: Map<string, import("react-msaview").DomainBand[]>;
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  readonly domainBandsByStart: Map<string, import("react-msaview").DomainBand[]>;
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- readonly mouseOverDomains: import("react-msaview").Annotation[];
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+ readonly mouseOverDomains: import("msa-parsers").Annotation[];
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  readonly referenceRowIndex: number | undefined;
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  readonly hoveredRowIndices: number[];
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  readonly highlightedColumnRuns: {
@@ -903,13 +904,13 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
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  x: "column" | "position";
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  kind: "features";
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  field?: string | undefined;
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- colors: Map<import("react-msaview").Annotation, {
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+ colors: Map<import("msa-parsers").Annotation, {
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  fill: string;
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  stroke: string;
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  }>;
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  legend: import("react-msaview").LegendEntry[];
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  legendTitle?: string | undefined;
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- labels?: Map<import("react-msaview").Annotation, string> | undefined;
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+ labels?: Map<import("msa-parsers").Annotation, string> | undefined;
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  })[];
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  readonly resolvedRowPanels: import("react-msaview").ResolvedRowPanel[];
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  readonly featureAlignShifts: Map<string, Map<string, number>>;
@@ -1140,7 +1141,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
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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("react-msaview").MSAFormat>>;
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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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  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]>;
@@ -1509,7 +1510,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
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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" | "connectedViewId" | "connectedFeature" | "connectedTranscript" | "blastParams" | "orthologParams" | "querySeqOffset" | "uniprotId" | "zoomToBaseLevel" | "dataStoreId" | "mafRegion"> & {
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+ }, "init" | "querySeqName" | "launchCompleted" | "embeddedMode" | "connectedViewId" | "connectedFeature" | "connectedTranscript" | "blastParams" | "orthologParams" | "querySeqOffset" | "uniprotId" | "zoomToBaseLevel" | "dataStoreId" | "mafRegion"> & {
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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>>;
@@ -1523,12 +1524,13 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
1523
1524
  dataStoreId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
1524
1525
  launchCompleted: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
1525
1526
  mafRegion: import("@jbrowse/mobx-state-tree").IType<MafRegion | undefined, MafRegion | undefined, MafRegion | undefined>;
1527
+ embeddedMode: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
1526
1528
  }>, "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"> & ({
1527
1529
  bgColor: boolean;
1528
1530
  colorSchemeName: string;
1529
1531
  customColorScheme: Record<string, string> | undefined;
1530
1532
  showColumnStats: boolean;
1531
- msaFormat: import("react-msaview").MSAFormat | undefined;
1533
+ msaFormat: import("msa-parsers").MSAFormat | undefined;
1532
1534
  drawLabels: boolean;
1533
1535
  labelsAlignRight: boolean;
1534
1536
  treeAreaWidth: number | undefined;
@@ -1665,7 +1667,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
1665
1667
  colorSchemeName: string;
1666
1668
  customColorScheme: Record<string, string> | undefined;
1667
1669
  showColumnStats: boolean;
1668
- msaFormat: import("react-msaview").MSAFormat | undefined;
1670
+ msaFormat: import("msa-parsers").MSAFormat | undefined;
1669
1671
  drawLabels: boolean;
1670
1672
  labelsAlignRight: boolean;
1671
1673
  treeAreaWidth: number | undefined;
@@ -99,6 +99,13 @@ export default function stateModelFactory() {
99
99
  * #property
100
100
  */
101
101
  mafRegion: types.frozen(),
102
+ /**
103
+ * #property
104
+ * react-msaview draws the toolbar's menus and Settings as icons, since
105
+ * a JBrowse view shares its row with other panels. A session spec sets
106
+ * it false for the labeled toolbar.
107
+ */
108
+ embeddedMode: true,
102
109
  }))
103
110
  .volatile(() => ({
104
111
  /**
@@ -163,3 +163,6 @@ describe('returning to the import form', () => {
163
163
  expect(model.dataStoreId).toBeUndefined();
164
164
  });
165
165
  });
166
+ test('the view asks react-msaview for its icon toolbar', () => {
167
+ expect(view().embeddedMode).toBe(true);
168
+ });
@@ -1,2 +1,2 @@
1
- import{a as l}from"./chunk-6EOYBBT4.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-447TIFAW.js.map
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
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "version": 3,
3
- "sources": ["../../node_modules/.pnpm/react-msaview@9.1.0_3e54acfe76b6ad0d26e91cd532b7f775/node_modules/react-msaview/src/components/dialogs/AboutDialog.tsx"],
3
+ "sources": ["../../node_modules/.pnpm/react-msaview@9.1.0_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
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6
6
  "names": ["import_react", "import_ui", "import_material", "AboutDialog", "onClose", "React", "version"]
@@ -0,0 +1,2 @@
1
+ import{i as E}from"./chunk-XXCNVFGP.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),d=i(x(),1);async function T(o){let l=await fetch(o);if(!l.ok)throw new Error(`HTTP ${l.status} fetching ${o} ${await l.text()}`);return l.text()}var b=(0,d.observer)(function({handleClose:o,model:l}){let[a,h]=(0,e.useState)(),[r,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:()=>{o()},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("div",{style:{display:"flex",margin:30}},e.default.createElement(t.FormControl,{component:"fieldset"},e.default.createElement(t.RadioGroup,{value:r,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"}))),r==="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)}})),a?e.default.createElement(t.Typography,null,a.name):null))),e.default.createElement(t.DialogActions,null,e.default.createElement(t.Button,{variant:"contained",color:"primary",disabled:v||(r==="file"?!a:!s.trim()),onClick:()=>{(async()=>{f(!0),u(void 0);try{let n=await(r==="file"&&a?a.text():T(s));l.setGFFFilehandle(void 0),l.setGFF(E(n)),l.setShowDomains(!0),o()}catch(n){console.error(n),u(n)}finally{f(!1)}})()}},"Open annotations"),e.default.createElement(t.Button,{variant:"contained",color:"secondary",onClick:()=>{o()}},"Cancel")))}),R=b;export{R as default};
2
+ //# sourceMappingURL=AnnotationFileDialog-CPJ4X7XW.js.map
@@ -1,7 +1,7 @@
1
1
  {
2
2
  "version": 3,
3
- "sources": ["../../node_modules/.pnpm/react-msaview@9.1.0_3e54acfe76b6ad0d26e91cd532b7f775/node_modules/react-msaview/src/components/dialogs/AnnotationFileDialog.tsx"],
3
+ "sources": ["../../node_modules/.pnpm/react-msaview@9.1.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/components/dialogs/AnnotationFileDialog.tsx"],
4
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 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\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 </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 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
6
  "names": ["import_react", "import_ui", "import_material", "import_mobx_react", "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
7
  }
@@ -1,2 +1,2 @@
1
- import{a as p}from"./chunk-ERCMNTEQ.js";import{X as v,Y as y}from"./chunk-OVAXNTPN.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-7ZHKKQ7W.js.map
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
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "version": 3,
3
- "sources": ["../../node_modules/.pnpm/react-msaview@9.1.0_3e54acfe76b6ad0d26e91cd532b7f775/node_modules/react-msaview/src/components/dialogs/ExportSVGDialog.tsx"],
3
+ "sources": ["../../node_modules/.pnpm/react-msaview@9.1.0_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"],
5
5
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6
6
  "names": ["import_react", "import_ui", "import_material", "import_mobx_react", "afterPaint", "fn", "ExportSVGDialog", "model", "onClose", "includeMinimap", "setIncludeMinimap", "includeTracks", "setIncludeTracks", "exportType", "setExportType", "error", "setError", "exporting", "setExporting", "theme", "turnedOnTracks", "numColumns", "leaves", "showMsaLetters", "hasTracks", "entire", "exportPageSize", "getLayout", "glyphs", "isLargeExport", "React", "Checkbox2", "event", "value", "e", "ExportSVGDialog_default"]
@@ -1,2 +1,2 @@
1
1
  import{a as C}from"./chunk-CVLB4VFP.js";import{a as F}from"./chunk-DNFD5II2.js";import{a as k}from"./chunk-BX4Z274Q.js";import{a as T}from"./chunk-J6KYLXRD.js";import{b as c}from"./chunk-FY3BTKY4.js";var e=c(T(),1),p=c(F(),1),t=c(k(),1),s=c(C(),1);function w(n,a){return[n.accession,n.name,n.description].some(o=>o?.toLowerCase().includes(a))}var x=(0,s.observer)(function({model:n,accessions:a}){let o=u=>{for(let m of a)n.setFilter(m,u)};return e.default.createElement("div",null,e.default.createElement(t.Button,{onClick:()=>{o(!0)}},"Toggle all on"),e.default.createElement(t.Button,{onClick:()=>{o(!1)}},"Toggle all off"))}),v=(0,s.observer)(function({model:n}){let{annotationTypes:a,annotations:o,featureColors:u,fillPalette:m}=n,[f,h]=(0,e.useState)(""),g=f.trim().toLowerCase(),d=[...a.values()].filter(l=>!g||w(l,g)),i=new Map,E=new Map;for(let l of o){let{accession:r}=l;i.set(r,(i.get(r)??0)+1),E.has(r)||E.set(r,u.get(l)?.fill??m[r])}return e.default.createElement(e.default.Fragment,null,e.default.createElement(t.TextField,{label:"Filter",size:"small",value:f,onChange:l=>{h(l.target.value)}}),e.default.createElement(x,{model:n,accessions:d.map(l=>l.accession)}),e.default.createElement(t.Table,{size:"small"},e.default.createElement(t.TableHead,null,e.default.createElement(t.TableRow,null,e.default.createElement(t.TableCell,{padding:"checkbox"}),e.default.createElement(t.TableCell,null,"color"),e.default.createElement(t.TableCell,null,"accession"),e.default.createElement(t.TableCell,null,"name"),e.default.createElement(t.TableCell,null,"count"),e.default.createElement(t.TableCell,null,"description"))),e.default.createElement(t.TableBody,null,d.map(({accession:l,name:r,description:b})=>e.default.createElement(t.TableRow,{key:l},e.default.createElement(t.TableCell,{padding:"checkbox"},e.default.createElement(t.Checkbox,{checked:!n.turnedOffFeatures.get(l),onChange:()=>{n.setFilter(l,!!n.turnedOffFeatures.get(l))}})),e.default.createElement(t.TableCell,null,e.default.createElement("div",{style:{width:20,height:20,background:E.get(l)}})),e.default.createElement(t.TableCell,null,l),e.default.createElement(t.TableCell,null,r),e.default.createElement(t.TableCell,null,i.get(l)),e.default.createElement(t.TableCell,null,b))))))}),y=(0,s.observer)(function({onClose:n,model:a}){return e.default.createElement(p.Dialog,{onClose:()=>{n()},open:!0,title:"Feature filters",maxWidth:"xl"},e.default.createElement(t.DialogContent,null,e.default.createElement(v,{model:a})))}),D=y;export{D as default};
2
- //# sourceMappingURL=FeatureDialog-EEOGSLOG.js.map
2
+ //# sourceMappingURL=FeatureDialog-NBDB5SWU.js.map
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "version": 3,
3
- "sources": ["../../node_modules/.pnpm/react-msaview@9.1.0_3e54acfe76b6ad0d26e91cd532b7f775/node_modules/react-msaview/src/components/dialogs/FeatureDialog.tsx"],
3
+ "sources": ["../../node_modules/.pnpm/react-msaview@9.1.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/components/dialogs/FeatureDialog.tsx"],
4
4
  "sourcesContent": ["import React, { useState } from 'react'\n\nimport { Dialog } from '@jbrowse/core/ui'\nimport {\n Button,\n Checkbox,\n DialogContent,\n Table,\n TableBody,\n TableCell,\n TableHead,\n TableRow,\n TextField,\n} from '@mui/material'\nimport { observer } from 'mobx-react'\n\nimport type { MsaViewModel } from '../../model.ts'\nimport type { Annotation } from '../../types.ts'\n\nfunction matches(type: Annotation, query: string) {\n return [type.accession, type.name, type.description].some(field =>\n field?.toLowerCase().includes(query),\n )\n}\n\nconst Toggles = observer(function ({\n model,\n accessions,\n}: {\n model: MsaViewModel\n accessions: string[]\n}) {\n const setAll = (shown: boolean) => {\n for (const accession of accessions) {\n model.setFilter(accession, shown)\n }\n }\n return (\n <div>\n <Button\n onClick={() => {\n setAll(true)\n }}\n >\n Toggle all on\n </Button>\n\n <Button\n onClick={() => {\n setAll(false)\n }}\n >\n Toggle all off\n </Button>\n </div>\n )\n})\n\nconst FeatureTable = observer(function ({ model }: { model: MsaViewModel }) {\n const { annotationTypes, annotations, featureColors, fillPalette } = model\n const [query, setQuery] = useState('')\n const needle = query.trim().toLowerCase()\n const types = [...annotationTypes.values()].filter(\n type => !needle || matches(type, needle),\n )\n const counts = new Map<string, number>()\n const swatches = new Map<string, string>()\n for (const annot of annotations) {\n const { accession } = annot\n counts.set(accession, (counts.get(accession) ?? 0) + 1)\n if (!swatches.has(accession)) {\n swatches.set(\n accession,\n featureColors.get(annot)?.fill ?? fillPalette[accession]!,\n )\n }\n }\n return (\n <>\n <TextField\n label=\"Filter\"\n size=\"small\"\n value={query}\n onChange={event => {\n setQuery(event.target.value)\n }}\n />\n <Toggles model={model} accessions={types.map(t => t.accession)} />\n <Table size=\"small\">\n <TableHead>\n <TableRow>\n <TableCell padding=\"checkbox\" />\n <TableCell>color</TableCell>\n <TableCell>accession</TableCell>\n <TableCell>name</TableCell>\n <TableCell>count</TableCell>\n <TableCell>description</TableCell>\n </TableRow>\n </TableHead>\n <TableBody>\n {types.map(({ accession, name, description }) => (\n <TableRow key={accession}>\n <TableCell padding=\"checkbox\">\n <Checkbox\n checked={!model.turnedOffFeatures.get(accession)}\n onChange={() => {\n model.setFilter(\n accession,\n !!model.turnedOffFeatures.get(accession),\n )\n }}\n />\n </TableCell>\n <TableCell>\n <div\n style={{\n width: 20,\n height: 20,\n background: swatches.get(accession),\n }}\n />\n </TableCell>\n <TableCell>{accession}</TableCell>\n <TableCell>{name}</TableCell>\n <TableCell>{counts.get(accession)}</TableCell>\n <TableCell>{description}</TableCell>\n </TableRow>\n ))}\n </TableBody>\n </Table>\n </>\n )\n})\n\nconst FeatureTypeDialog = observer(function ({\n onClose,\n model,\n}: {\n onClose: () => void\n model: MsaViewModel\n}) {\n return (\n <Dialog\n onClose={() => {\n onClose()\n }}\n open\n title=\"Feature filters\"\n maxWidth=\"xl\"\n >\n <DialogContent>\n <FeatureTable model={model} />\n </DialogContent>\n </Dialog>\n )\n})\n\nexport default FeatureTypeDialog\n"],
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6
6
  "names": ["import_react", "import_ui", "import_material", "import_mobx_react", "matches", "type", "query", "field", "Toggles", "model", "accessions", "setAll", "shown", "accession", "React", "FeatureTable", "annotationTypes", "annotations", "featureColors", "fillPalette", "setQuery", "needle", "types", "counts", "swatches", "annot", "event", "t", "name", "description", "FeatureTypeDialog", "onClose", "FeatureDialog_default"]
@@ -1,2 +1,2 @@
1
- import{a as n}from"./chunk-6EOYBBT4.js";import{a as i,b as m}from"./chunk-TSHN6J7U.js";import{a as E}from"./chunk-DNFD5II2.js";import{a as b}from"./chunk-BX4Z274Q.js";import{a as p}from"./chunk-J6KYLXRD.js";import{b as a}from"./chunk-FY3BTKY4.js";var e=a(p(),1),u=a(E(),1),t=a(b(),1);var f=(0,e.lazy)(()=>import("./AboutDialog-447TIFAW.js"));function c({title:o,rows:l}){return e.default.createElement(e.default.Fragment,null,e.default.createElement(t.Typography,{variant:"subtitle2",sx:{mt:1}},o),e.default.createElement(t.Table,{size:"small","aria-label":o},e.default.createElement(t.TableBody,null,l.map(({label:r,action:s})=>e.default.createElement(t.TableRow,{key:r},e.default.createElement(t.TableCell,{sx:{whiteSpace:"nowrap",fontWeight:500}},r),e.default.createElement(t.TableCell,null,s))))))}function g({model:o,onClose:l}){return e.default.createElement(u.Dialog,{open:!0,title:"Mouse & keyboard",onClose:l},e.default.createElement(t.DialogContent,null,e.default.createElement(c,{title:"Mouse",rows:m}),e.default.createElement(c,{title:"Keyboard (click the alignment first)",rows:i})),e.default.createElement(t.DialogActions,null,e.default.createElement(t.Typography,{variant:"caption",sx:{mr:"auto",pl:1}},"MSAView ",n),e.default.createElement(t.Button,{onClick:()=>{o.queueDialog(r=>[f,{onClose:r}]),l()}},"About & credits"),e.default.createElement(t.Button,{variant:"contained",onClick:l},"Close")))}export{g as default};
2
- //# sourceMappingURL=HelpDialog-TCWNBZOV.js.map
1
+ import{a as n}from"./chunk-XTQQNBQ5.js";import{a as i,b as m}from"./chunk-JDQUBCHM.js";import{a as E}from"./chunk-DNFD5II2.js";import{a as b}from"./chunk-BX4Z274Q.js";import{a as p}from"./chunk-J6KYLXRD.js";import{b as a}from"./chunk-FY3BTKY4.js";var e=a(p(),1),u=a(E(),1),t=a(b(),1);var f=(0,e.lazy)(()=>import("./AboutDialog-HCCCEJ6V.js"));function c({title:o,rows:l}){return e.default.createElement(e.default.Fragment,null,e.default.createElement(t.Typography,{variant:"subtitle2",sx:{mt:1}},o),e.default.createElement(t.Table,{size:"small","aria-label":o},e.default.createElement(t.TableBody,null,l.map(({label:r,action:s})=>e.default.createElement(t.TableRow,{key:r},e.default.createElement(t.TableCell,{sx:{whiteSpace:"nowrap",fontWeight:500}},r),e.default.createElement(t.TableCell,null,s))))))}function g({model:o,onClose:l}){return e.default.createElement(u.Dialog,{open:!0,title:"Mouse & keyboard",onClose:l},e.default.createElement(t.DialogContent,null,e.default.createElement(c,{title:"Mouse",rows:m}),e.default.createElement(c,{title:"Keyboard (click the alignment first)",rows:i})),e.default.createElement(t.DialogActions,null,e.default.createElement(t.Typography,{variant:"caption",sx:{mr:"auto",pl:1}},"MSAView ",n),e.default.createElement(t.Button,{onClick:()=>{o.queueDialog(r=>[f,{onClose:r}]),l()}},"About & credits"),e.default.createElement(t.Button,{variant:"contained",onClick:l},"Close")))}export{g as default};
2
+ //# sourceMappingURL=HelpDialog-UCUYPCOI.js.map
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "version": 3,
3
- "sources": ["../../node_modules/.pnpm/react-msaview@9.1.0_3e54acfe76b6ad0d26e91cd532b7f775/node_modules/react-msaview/src/components/dialogs/HelpDialog.tsx"],
3
+ "sources": ["../../node_modules/.pnpm/react-msaview@9.1.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/components/dialogs/HelpDialog.tsx"],
4
4
  "sourcesContent": ["import React, { lazy } from 'react'\n\nimport { Dialog } from '@jbrowse/core/ui'\nimport {\n Button,\n DialogActions,\n DialogContent,\n Table,\n TableBody,\n TableCell,\n TableRow,\n Typography,\n} from '@mui/material'\n\nimport { version } from '../../version.ts'\nimport { keyboardControls, mouseControls } from '../controls.ts'\n\nimport type { MsaViewModel } from '../../model.ts'\nimport type { Control } from '../controls.ts'\n\nconst AboutDialog = lazy(() => import('./AboutDialog.tsx'))\n\nfunction ControlTable({ title, rows }: { title: string; rows: Control[] }) {\n return (\n <>\n <Typography variant=\"subtitle2\" sx={{ mt: 1 }}>\n {title}\n </Typography>\n <Table size=\"small\" aria-label={title}>\n <TableBody>\n {rows.map(({ label, action }) => (\n <TableRow key={label}>\n <TableCell sx={{ whiteSpace: 'nowrap', fontWeight: 500 }}>\n {label}\n </TableCell>\n <TableCell>{action}</TableCell>\n </TableRow>\n ))}\n </TableBody>\n </Table>\n </>\n )\n}\n\nexport default function HelpDialog({\n model,\n onClose,\n}: {\n model: MsaViewModel\n onClose: () => void\n}) {\n return (\n <Dialog open title=\"Mouse & keyboard\" onClose={onClose}>\n <DialogContent>\n <ControlTable title=\"Mouse\" rows={mouseControls} />\n <ControlTable\n title=\"Keyboard (click the alignment first)\"\n rows={keyboardControls}\n />\n </DialogContent>\n <DialogActions>\n <Typography variant=\"caption\" sx={{ mr: 'auto', pl: 1 }}>\n MSAView {version}\n </Typography>\n <Button\n onClick={() => {\n model.queueDialog(done => [AboutDialog, { onClose: done }])\n onClose()\n }}\n >\n About & credits\n </Button>\n <Button variant=\"contained\" onClick={onClose}>\n Close\n </Button>\n </DialogActions>\n </Dialog>\n )\n}\n"],
5
5
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2
2
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  `)??"",[$]),J=Me(ue,I),Pe=vo(J,`${F??""}_${c[0]??""}`),er=M??x??P.error??l;return T.default.createElement(T.default.Fragment,null,T.default.createElement(Y,{error:er},T.default.createElement(g,{select:!0,label:"Select MSA dataset",value:m,onChange:B=>{b(B.target.value)}},d?.map(B=>T.default.createElement(Re.MenuItem,{key:B.datasetId,value:B.datasetId},B.name))),S?T.default.createElement("div",{className:i.selectedContainer},!j&&_?T.default.createElement(Ce.LoadingEllipses,{variant:"h6",message:`Loading MSA for ${fe(C)||F}`}):null,j?T.default.createElement(Ce.LoadingEllipses,{variant:"h6",message:`Loading available MSAs for (${S.name})`}):null,v?T.default.createElement("div",null,T.default.createElement(Ce.SanitizedHTML,{html:S.description}),T.default.createElement(R,{feature:t,...P}),ue?T.default.createElement(he,{...J,querySeqName:Pe}):null):null):null),T.default.createElement(X,{model:e,hint:_?T.default.createElement(Ce.LoadingEllipses,{message:"Loading alignment"}):$?.length&&!Pe?T.default.createElement(Re.Typography,{color:"textSecondary",variant:"body2"},"no row matches this transcript"):T.default.createElement(ie,{status:k}),submitDisabled:!C||!$?.length||!Pe,onSubmit:B=>{C&&ue&&p(()=>Q({view:a,feature:C,placement:B,displayName:te(C),drawNodeBubbles:!1,labelsAlignRight:!0,showBranchLen:!1,colWidth:10,rowHeight:12,colorSchemeName:"percent_identity_dynamic",querySeqName:Pe,querySeqOffset:J.querySeqOffset,data:{msa:ue}}))},onCancel:o}))}),Xo=Wr;var et=s(f());function Le({children:e,value:t,index:o}){let r=t===o,[n,a]=(0,et.useState)(r);return r&&!n&&a(!0),et.default.createElement("div",{role:"tabpanel",hidden:!r},n||r?e:null)}function Ur({handleClose:e,feature:t,model:o,preferredTranscriptId:r}){let n=(0,Ro.getSession)(o),i=!!Xe(n.jbrowse)?.length,[u,c]=(0,A.useState)("orthologs");return A.default.createElement(Zo.Dialog,{maxWidth:"xl",title:"Launch MSA view",open:!0,onClose:e},A.default.createElement(Wt,null,A.default.createElement("div",{style:{display:"flex",alignItems:"center"}},A.default.createElement(ye.Tabs,{value:u,onChange:(l,p)=>{c(p)}},A.default.createElement(ye.Tab,{label:"Orthologs",value:"orthologs"}),A.default.createElement(ye.Tab,{label:"BLAST query",value:"ncbi_blast"}),i?A.default.createElement(ye.Tab,{label:"Pre-loaded MSA datasets",value:"preloaded_msa"}):null,A.default.createElement(ye.Tab,{label:"Manual upload",value:"manual_msa"})),A.default.createElement(ct,null)),A.default.createElement(Le,{value:u,index:"orthologs"},A.default.createElement(Vo,{handleClose:e,feature:t,model:o,preferredTranscriptId:r})),A.default.createElement(Le,{value:u,index:"ncbi_blast"},A.default.createElement(ut,{handleClose:e,feature:t,model:o,preferredTranscriptId:r})),i?A.default.createElement(Le,{value:u,index:"preloaded_msa"},A.default.createElement(Xo,{model:o,feature:t,handleClose:e,preferredTranscriptId:r})):null,A.default.createElement(Le,{value:u,index:"manual_msa"},A.default.createElement(Po,{model:o,feature:t,handleClose:e,preferredTranscriptId:r}))))}export{Ur as default};
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