jbrowse-plugin-msaview 2.6.8 → 2.7.1

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Files changed (11) hide show
  1. package/dist/LaunchMsaView/index.js +19 -11
  2. package/dist/MsaViewPanel/model.d.ts +446 -144
  3. package/dist/MsaViewPanel/model.js +10 -1
  4. package/dist/jbrowse-plugin-msaview.umd.production.min.js +67 -29
  5. package/dist/jbrowse-plugin-msaview.umd.production.min.js.map +4 -4
  6. package/dist/version.d.ts +1 -1
  7. package/dist/version.js +1 -1
  8. package/package.json +20 -22
  9. package/src/LaunchMsaView/index.ts +62 -37
  10. package/src/MsaViewPanel/model.ts +10 -4
  11. package/src/version.ts +1 -1
package/dist/MsaViewPanel/model.d.ts CHANGED
@@ -29,41 +29,58 @@ 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").IType<boolean | undefined, boolean, boolean>;
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- }, "height" | "id" | "type" | "drawLabels" | "labelsAlignRight" | "treeAreaWidth" | "treeWidth" | "showBranchLen" | "drawTree" | "drawNodeBubbles" | "bgColor" | "colorSchemeName" | "msaFormat" | "data" | "showDomains" | "hideGaps" | "allowedGappyness" | "subFeatureRows" | "drawMsaLetters" | "scrollZoom" | "rowHeight" | "scrollY" | "scrollX" | "colWidth" | "currentAlignment" | "treeFilehandle" | "msaFilehandle" | "treeMetadataFilehandle" | "gffFilehandle" | "collapsed" | "showOnly" | "turnedOffTracks" | "featureFilters" | "relativeTo" | "highlightColumns"> & Omit<Omit<Omit<{}, "drawLabels" | "labelsAlignRight" | "treeAreaWidth" | "treeWidth" | "showBranchLen" | "drawTree" | "drawNodeBubbles"> & {
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- drawLabels: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
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- labelsAlignRight: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
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+ }, "height" | "id" | "type" | "drawLabels" | "labelsAlignRight" | "treeAreaWidth" | "treeWidth" | "showBranchLen" | "drawTree" | "drawNodeBubbles" | "autoTreeAreaWidth" | "bgColor" | "colorSchemeName" | "showColumnStats" | "msaFormat" | "data" | "showDomains" | "hideGaps" | "allowedGappyness" | "subFeatureRows" | "drawMsaLetters" | "scrollZoom" | "rowHeight" | "scrollY" | "scrollX" | "colWidth" | "treeFilehandle" | "msaFilehandle" | "treeMetadataFilehandle" | "gffFilehandle" | "currentAlignment" | "collapsed" | "showOnly" | "turnedOffTracks" | "featureFilters" | "relativeTo" | "highlightColumns"> & Omit<Omit<Omit<{}, "drawLabels" | "labelsAlignRight" | "treeAreaWidth" | "treeWidth" | "showBranchLen" | "drawTree" | "drawNodeBubbles" | "autoTreeAreaWidth"> & {
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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").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
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  treeWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
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- showBranchLen: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
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- drawTree: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
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- drawNodeBubbles: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
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- }, "bgColor" | "colorSchemeName" | "msaFormat"> & {
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- bgColor: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
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- colorSchemeName: import("@jbrowse/mobx-state-tree").IType<string | undefined, string, string>;
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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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- }, "height" | "id" | "type" | "data" | "showDomains" | "hideGaps" | "allowedGappyness" | "subFeatureRows" | "drawMsaLetters" | "scrollZoom" | "rowHeight" | "scrollY" | "scrollX" | "colWidth" | "currentAlignment" | "treeFilehandle" | "msaFilehandle" | "treeMetadataFilehandle" | "gffFilehandle" | "collapsed" | "showOnly" | "turnedOffTracks" | "featureFilters" | "relativeTo" | "highlightColumns"> & {
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+ showBranchLen: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
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+ drawTree: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
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+ drawNodeBubbles: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
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+ autoTreeAreaWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
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+ }, "bgColor" | "colorSchemeName" | "showColumnStats" | "msaFormat"> & {
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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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+ 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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+ }, "height" | "id" | "type" | "data" | "showDomains" | "hideGaps" | "allowedGappyness" | "subFeatureRows" | "drawMsaLetters" | "scrollZoom" | "rowHeight" | "scrollY" | "scrollX" | "colWidth" | "treeFilehandle" | "msaFilehandle" | "treeMetadataFilehandle" | "gffFilehandle" | "currentAlignment" | "collapsed" | "showOnly" | "turnedOffTracks" | "featureFilters" | "relativeTo" | "highlightColumns"> & {
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  id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
46
- showDomains: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
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- hideGaps: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
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- allowedGappyness: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
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- subFeatureRows: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
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+ showDomains: 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").ISimpleType<"MsaView">;
51
- drawMsaLetters: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
52
- scrollZoom: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
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+ drawMsaLetters: 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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  height: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
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- rowHeight: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
55
- scrollY: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
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- scrollX: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
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- colWidth: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
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- treeFilehandle: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").ITypeUnion<any, {
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+ rowHeight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
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+ scrollY: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
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+ scrollX: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
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+ colWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
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+ treeFilehandle: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").ITypeUnion<import("@jbrowse/mobx-state-tree").ModelCreationType<{
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+ locationType: "LocalPathLocation";
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+ localPath: string;
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+ }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
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+ locationType: "BlobLocation";
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+ name: string;
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+ blobId: string;
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+ }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
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+ locationType: "FileHandleLocation";
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+ name: string;
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+ handleId: string;
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+ }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
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  locationType: "UriLocation";
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  uri: string;
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+ baseUri: string | undefined;
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  internetAccountId: string | undefined;
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- internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
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- internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
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- authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
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+ internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelCreationType<{
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+ internetAccountType: string;
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+ authInfo: any;
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  }> | undefined;
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- } | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
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+ }>, import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
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+ locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
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+ localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
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+ }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
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  locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
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  name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
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  blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
@@ -71,11 +88,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
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  locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
72
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  name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
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  handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
74
- }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
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- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
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- localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
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- }>, any>, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
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- msaFilehandle: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").ITypeUnion<any, {
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+ }> | {
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  locationType: "UriLocation";
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  uri: string;
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  internetAccountId: string | undefined;
@@ -83,7 +96,85 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
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  internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
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  authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
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  }> | undefined;
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- } | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
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+ }, ({
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+ locationType: "UriLocation";
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+ uri: string;
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+ } & Partial<{
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+ locationType: "UriLocation";
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+ uri: string;
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+ baseUri: string | undefined;
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+ internetAccountId: string | undefined;
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+ internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelCreationType<{
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+ internetAccountType: string;
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+ authInfo: any;
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+ }> | undefined;
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+ }>) | ({
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+ blobId: string;
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+ locationType: "BlobLocation";
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+ name: string;
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+ } & Partial<{
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+ locationType: "BlobLocation";
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+ name: string;
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+ blobId: string;
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+ }>) | ({
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+ handleId: string;
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+ locationType: "FileHandleLocation";
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+ name: string;
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+ } & Partial<{
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+ locationType: "FileHandleLocation";
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+ name: string;
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+ handleId: string;
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+ }>) | ({
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+ localPath: string;
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+ locationType: "LocalPathLocation";
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+ } & Partial<{
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+ locationType: "LocalPathLocation";
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+ localPath: string;
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+ }>)>, import("@jbrowse/core/util/types/mst").LegacyFileLocation | import("@jbrowse/mobx-state-tree").ModelCreationType<{
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+ locationType: "LocalPathLocation";
135
+ localPath: string;
136
+ }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
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+ locationType: "BlobLocation";
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+ name: string;
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+ blobId: string;
140
+ }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
141
+ locationType: "FileHandleLocation";
142
+ name: string;
143
+ handleId: string;
144
+ }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
145
+ locationType: "UriLocation";
146
+ uri: string;
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+ baseUri: string | undefined;
148
+ internetAccountId: string | undefined;
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+ internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelCreationType<{
150
+ internetAccountType: string;
151
+ authInfo: any;
152
+ }> | undefined;
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+ }>, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
154
+ msaFilehandle: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").ITypeUnion<import("@jbrowse/mobx-state-tree").ModelCreationType<{
155
+ locationType: "LocalPathLocation";
156
+ localPath: string;
157
+ }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
158
+ locationType: "BlobLocation";
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+ name: string;
160
+ blobId: string;
161
+ }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
162
+ locationType: "FileHandleLocation";
163
+ name: string;
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+ handleId: string;
165
+ }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
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+ locationType: "UriLocation";
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+ uri: string;
168
+ baseUri: string | undefined;
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+ internetAccountId: string | undefined;
170
+ internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelCreationType<{
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+ internetAccountType: string;
172
+ authInfo: any;
173
+ }> | undefined;
174
+ }>, import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
175
+ locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
176
+ localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
177
+ }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
87
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  locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
88
179
  name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
89
180
  blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
@@ -91,11 +182,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
91
182
  locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
92
183
  name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
93
184
  handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
94
- }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
95
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
96
- localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
97
- }>, any>, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
98
- treeMetadataFilehandle: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").ITypeUnion<any, {
185
+ }> | {
99
186
  locationType: "UriLocation";
100
187
  uri: string;
101
188
  internetAccountId: string | undefined;
@@ -103,7 +190,85 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
103
190
  internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
104
191
  authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
105
192
  }> | undefined;
106
- } | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
193
+ }, ({
194
+ locationType: "UriLocation";
195
+ uri: string;
196
+ } & Partial<{
197
+ locationType: "UriLocation";
198
+ uri: string;
199
+ baseUri: string | undefined;
200
+ internetAccountId: string | undefined;
201
+ internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelCreationType<{
202
+ internetAccountType: string;
203
+ authInfo: any;
204
+ }> | undefined;
205
+ }>) | ({
206
+ blobId: string;
207
+ locationType: "BlobLocation";
208
+ name: string;
209
+ } & Partial<{
210
+ locationType: "BlobLocation";
211
+ name: string;
212
+ blobId: string;
213
+ }>) | ({
214
+ handleId: string;
215
+ locationType: "FileHandleLocation";
216
+ name: string;
217
+ } & Partial<{
218
+ locationType: "FileHandleLocation";
219
+ name: string;
220
+ handleId: string;
221
+ }>) | ({
222
+ localPath: string;
223
+ locationType: "LocalPathLocation";
224
+ } & Partial<{
225
+ locationType: "LocalPathLocation";
226
+ localPath: string;
227
+ }>)>, import("@jbrowse/core/util/types/mst").LegacyFileLocation | import("@jbrowse/mobx-state-tree").ModelCreationType<{
228
+ locationType: "LocalPathLocation";
229
+ localPath: string;
230
+ }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
231
+ locationType: "BlobLocation";
232
+ name: string;
233
+ blobId: string;
234
+ }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
235
+ locationType: "FileHandleLocation";
236
+ name: string;
237
+ handleId: string;
238
+ }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
239
+ locationType: "UriLocation";
240
+ uri: string;
241
+ baseUri: string | undefined;
242
+ internetAccountId: string | undefined;
243
+ internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelCreationType<{
244
+ internetAccountType: string;
245
+ authInfo: any;
246
+ }> | undefined;
247
+ }>, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
248
+ treeMetadataFilehandle: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").ITypeUnion<import("@jbrowse/mobx-state-tree").ModelCreationType<{
249
+ locationType: "LocalPathLocation";
250
+ localPath: string;
251
+ }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
252
+ locationType: "BlobLocation";
253
+ name: string;
254
+ blobId: string;
255
+ }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
256
+ locationType: "FileHandleLocation";
257
+ name: string;
258
+ handleId: string;
259
+ }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
260
+ locationType: "UriLocation";
261
+ uri: string;
262
+ baseUri: string | undefined;
263
+ internetAccountId: string | undefined;
264
+ internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelCreationType<{
265
+ internetAccountType: string;
266
+ authInfo: any;
267
+ }> | undefined;
268
+ }>, import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
269
+ locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
270
+ localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
271
+ }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
107
272
  locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
108
273
  name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
109
274
  blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
@@ -111,11 +276,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
111
276
  locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
112
277
  name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
113
278
  handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
114
- }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
115
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
116
- localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
117
- }>, any>, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
118
- gffFilehandle: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").ITypeUnion<any, {
279
+ }> | {
119
280
  locationType: "UriLocation";
120
281
  uri: string;
121
282
  internetAccountId: string | undefined;
@@ -123,7 +284,85 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
123
284
  internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
124
285
  authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
125
286
  }> | undefined;
126
- } | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
287
+ }, ({
288
+ locationType: "UriLocation";
289
+ uri: string;
290
+ } & Partial<{
291
+ locationType: "UriLocation";
292
+ uri: string;
293
+ baseUri: string | undefined;
294
+ internetAccountId: string | undefined;
295
+ internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelCreationType<{
296
+ internetAccountType: string;
297
+ authInfo: any;
298
+ }> | undefined;
299
+ }>) | ({
300
+ blobId: string;
301
+ locationType: "BlobLocation";
302
+ name: string;
303
+ } & Partial<{
304
+ locationType: "BlobLocation";
305
+ name: string;
306
+ blobId: string;
307
+ }>) | ({
308
+ handleId: string;
309
+ locationType: "FileHandleLocation";
310
+ name: string;
311
+ } & Partial<{
312
+ locationType: "FileHandleLocation";
313
+ name: string;
314
+ handleId: string;
315
+ }>) | ({
316
+ localPath: string;
317
+ locationType: "LocalPathLocation";
318
+ } & Partial<{
319
+ locationType: "LocalPathLocation";
320
+ localPath: string;
321
+ }>)>, import("@jbrowse/core/util/types/mst").LegacyFileLocation | import("@jbrowse/mobx-state-tree").ModelCreationType<{
322
+ locationType: "LocalPathLocation";
323
+ localPath: string;
324
+ }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
325
+ locationType: "BlobLocation";
326
+ name: string;
327
+ blobId: string;
328
+ }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
329
+ locationType: "FileHandleLocation";
330
+ name: string;
331
+ handleId: string;
332
+ }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
333
+ locationType: "UriLocation";
334
+ uri: string;
335
+ baseUri: string | undefined;
336
+ internetAccountId: string | undefined;
337
+ internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelCreationType<{
338
+ internetAccountType: string;
339
+ authInfo: any;
340
+ }> | undefined;
341
+ }>, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
342
+ gffFilehandle: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").ITypeUnion<import("@jbrowse/mobx-state-tree").ModelCreationType<{
343
+ locationType: "LocalPathLocation";
344
+ localPath: string;
345
+ }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
346
+ locationType: "BlobLocation";
347
+ name: string;
348
+ blobId: string;
349
+ }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
350
+ locationType: "FileHandleLocation";
351
+ name: string;
352
+ handleId: string;
353
+ }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
354
+ locationType: "UriLocation";
355
+ uri: string;
356
+ baseUri: string | undefined;
357
+ internetAccountId: string | undefined;
358
+ internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelCreationType<{
359
+ internetAccountType: string;
360
+ authInfo: any;
361
+ }> | undefined;
362
+ }>, import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
363
+ locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
364
+ localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
365
+ }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
127
366
  locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
128
367
  name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
129
368
  blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
@@ -131,14 +370,73 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
131
370
  locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
132
371
  name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
133
372
  handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
134
- }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
135
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
136
- localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
137
- }>, any>, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
138
- currentAlignment: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
139
- collapsed: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
373
+ }> | {
374
+ locationType: "UriLocation";
375
+ uri: string;
376
+ internetAccountId: string | undefined;
377
+ internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
378
+ internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
379
+ authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
380
+ }> | undefined;
381
+ }, ({
382
+ locationType: "UriLocation";
383
+ uri: string;
384
+ } & Partial<{
385
+ locationType: "UriLocation";
386
+ uri: string;
387
+ baseUri: string | undefined;
388
+ internetAccountId: string | undefined;
389
+ internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelCreationType<{
390
+ internetAccountType: string;
391
+ authInfo: any;
392
+ }> | undefined;
393
+ }>) | ({
394
+ blobId: string;
395
+ locationType: "BlobLocation";
396
+ name: string;
397
+ } & Partial<{
398
+ locationType: "BlobLocation";
399
+ name: string;
400
+ blobId: string;
401
+ }>) | ({
402
+ handleId: string;
403
+ locationType: "FileHandleLocation";
404
+ name: string;
405
+ } & Partial<{
406
+ locationType: "FileHandleLocation";
407
+ name: string;
408
+ handleId: string;
409
+ }>) | ({
410
+ localPath: string;
411
+ locationType: "LocalPathLocation";
412
+ } & Partial<{
413
+ locationType: "LocalPathLocation";
414
+ localPath: string;
415
+ }>)>, import("@jbrowse/core/util/types/mst").LegacyFileLocation | import("@jbrowse/mobx-state-tree").ModelCreationType<{
416
+ locationType: "LocalPathLocation";
417
+ localPath: string;
418
+ }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
419
+ locationType: "BlobLocation";
420
+ name: string;
421
+ blobId: string;
422
+ }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
423
+ locationType: "FileHandleLocation";
424
+ name: string;
425
+ handleId: string;
426
+ }> | import("@jbrowse/mobx-state-tree").ModelCreationType<{
427
+ locationType: "UriLocation";
428
+ uri: string;
429
+ baseUri: string | undefined;
430
+ internetAccountId: string | undefined;
431
+ internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelCreationType<{
432
+ internetAccountType: string;
433
+ authInfo: any;
434
+ }> | undefined;
435
+ }>, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
436
+ currentAlignment: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
437
+ collapsed: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISimpleType<string>>, [undefined]>;
140
438
  showOnly: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
141
- turnedOffTracks: import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
439
+ turnedOffTracks: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>, [undefined]>;
142
440
  data: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IModelType<{
143
441
  tree: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
144
442
  msa: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
@@ -155,7 +453,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
155
453
  treeMetadata: string | undefined;
156
454
  gff: string | undefined;
157
455
  }>, [undefined]>;
158
- featureFilters: import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
456
+ featureFilters: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>, [undefined]>;
159
457
  relativeTo: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
160
458
  highlightColumns: import("@jbrowse/mobx-state-tree").IType<number[] | undefined, number[] | undefined, number[] | undefined>;
161
459
  }, "init" | "querySeqName" | "zoomToBaseLevel" | "connectedViewId" | "connectedFeature" | "blastParams" | "uniprotId" | "dataStoreId" | "mafRegion"> & {
@@ -189,13 +487,15 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
189
487
  setTreeWidth(n: number): void;
190
488
  setLabelsAlignRight(arg: boolean): void;
191
489
  setDrawTree(arg: boolean): void;
490
+ setAutoTreeAreaWidth(arg: boolean): void;
192
491
  setShowBranchLen(arg: boolean): void;
193
492
  setDrawNodeBubbles(arg: boolean): void;
194
493
  setDrawLabels(arg: boolean): void;
195
494
  } & {
196
495
  setColorSchemeName(name: string): void;
197
496
  setBgColor(arg: boolean): void;
198
- setMSAFormat(arg?: import("msa-parsers").MSAFormat): void;
497
+ setShowColumnStats(arg: boolean): void;
498
+ setMSAFormat(arg?: import("react-msaview").MSAFormat): void;
199
499
  } & {
200
500
  headerHeight: number;
201
501
  status: {
@@ -282,7 +582,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
282
582
  readonly noDomains: boolean;
283
583
  menuItems(): never[];
284
584
  readonly treeMetadata: any;
285
- readonly MSA: import("msa-parsers").MSAParserType | null;
585
+ readonly MSA: import("react-msaview").MSAParserType | null;
286
586
  readonly numColumns: number;
287
587
  readonly tree: import("react-msaview").NodeWithIds;
288
588
  readonly rowNames: string[];
@@ -304,12 +604,13 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
304
604
  }[]>;
305
605
  readonly rows: [string, string][];
306
606
  readonly numRows: number;
607
+ readonly seqPosGlobalColIndex: Map<string, Int32Array<ArrayBuffer>>;
307
608
  readonly rowMap: Map<string, string>;
308
609
  readonly columns: Map<string, string>;
309
610
  readonly columns2d: string[];
310
611
  readonly fontSize: number;
311
- readonly colStats: Record<string, number>[];
312
- readonly colStatsSums: number[];
612
+ readonly colStats: import("react-msaview").ColumnCounts;
613
+ readonly colStatsSums: Uint32Array<ArrayBufferLike>;
313
614
  readonly sequenceType: "dna" | "rna" | "amino";
314
615
  readonly colConsensus: {
315
616
  letter: string;
@@ -317,6 +618,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
317
618
  }[];
318
619
  readonly colClustalX: Record<string, string>[];
319
620
  readonly conservation: number[];
621
+ readonly propertyConservation: number[];
320
622
  readonly hierarchy: import("react-msaview").HierarchyNode<import("react-msaview").NodeWithIdsAndLength>;
321
623
  readonly totalHeight: number;
322
624
  readonly leaves: import("react-msaview").HierarchyNode<import("react-msaview").NodeWithIdsAndLength>[];
@@ -460,16 +762,27 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
460
762
  end: number;
461
763
  strand: number | undefined;
462
764
  }[];
463
- readonly mouseOverDomains: {
464
- id: string;
465
- name: string;
466
- accession: string;
467
- description: string;
468
- featureType: string | undefined;
765
+ readonly domainBands: Map<string, import("react-msaview").DomainBand[]>;
766
+ readonly domainBandsByStart: Map<string, import("react-msaview").DomainBand[]>;
767
+ readonly mouseOverDomains: import("react-msaview").TidyDomainAnnotation[];
768
+ readonly referenceRowIndex: number | undefined;
769
+ readonly hoveredRowIndices: number[];
770
+ readonly highlightedColumnRuns: {
469
771
  start: number;
470
772
  end: number;
471
- strand: number | undefined;
472
773
  }[];
774
+ readonly mouseOverColumnStats: {
775
+ col: number;
776
+ total: number;
777
+ gaps: number;
778
+ gapFraction: number;
779
+ conservation: number;
780
+ propertyConservation: number | undefined;
781
+ consensusLetter: string;
782
+ consensusCount: number;
783
+ consensusFraction: number;
784
+ distribution: [string, number][];
785
+ } | undefined;
473
786
  getRowData(name: string): {
474
787
  data: {
475
788
  name?: string;
@@ -621,41 +934,41 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
621
934
  id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
622
935
  displayName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
623
936
  minimized: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
624
- }> & Omit<import("@jbrowse/mobx-state-tree").ModelSnapshotType<Omit<Omit<Omit<{}, "drawLabels" | "labelsAlignRight" | "treeAreaWidth" | "treeWidth" | "showBranchLen" | "drawTree" | "drawNodeBubbles"> & {
625
- drawLabels: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
626
- labelsAlignRight: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
627
- treeAreaWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
628
- treeWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
629
- showBranchLen: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
630
- drawTree: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
631
- drawNodeBubbles: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
632
- }, "bgColor" | "colorSchemeName" | "msaFormat"> & {
633
- bgColor: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
634
- colorSchemeName: import("@jbrowse/mobx-state-tree").IType<string | undefined, string, string>;
635
- msaFormat: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<import("msa-parsers").MSAFormat>>;
636
- }, "height" | "id" | "type" | "data" | "showDomains" | "hideGaps" | "allowedGappyness" | "subFeatureRows" | "drawMsaLetters" | "scrollZoom" | "rowHeight" | "scrollY" | "scrollX" | "colWidth" | "currentAlignment" | "treeFilehandle" | "msaFilehandle" | "treeMetadataFilehandle" | "gffFilehandle" | "collapsed" | "showOnly" | "turnedOffTracks" | "featureFilters" | "relativeTo" | "highlightColumns"> & {
637
- id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
638
- showDomains: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
639
- hideGaps: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
640
- allowedGappyness: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
641
- subFeatureRows: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
642
- type: import("@jbrowse/mobx-state-tree").ISimpleType<"MsaView">;
643
- drawMsaLetters: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
644
- scrollZoom: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
645
- height: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
646
- rowHeight: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
647
- scrollY: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
648
- scrollX: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
649
- colWidth: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
650
- treeFilehandle: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").ITypeUnion<any, {
651
- locationType: "UriLocation";
652
- uri: string;
653
- internetAccountId: string | undefined;
654
- internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
655
- internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
656
- authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
657
- }> | undefined;
658
- } | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
937
+ }> & {
938
+ data: {
939
+ treeMetadata?: string | undefined;
940
+ msa?: string | undefined;
941
+ tree?: string | undefined;
942
+ };
943
+ drawLabels: boolean;
944
+ labelsAlignRight: boolean;
945
+ treeAreaWidth: number;
946
+ treeWidth: number;
947
+ showBranchLen: boolean;
948
+ drawTree: boolean;
949
+ drawNodeBubbles: boolean;
950
+ autoTreeAreaWidth: boolean;
951
+ bgColor: boolean;
952
+ colorSchemeName: string;
953
+ showColumnStats: boolean;
954
+ msaFormat: import("react-msaview").MSAFormat | undefined;
955
+ id: string;
956
+ showDomains: boolean;
957
+ hideGaps: boolean;
958
+ allowedGappyness: number;
959
+ subFeatureRows: boolean;
960
+ type: "MsaView";
961
+ drawMsaLetters: boolean;
962
+ scrollZoom: boolean;
963
+ height: number;
964
+ rowHeight: number;
965
+ scrollY: number;
966
+ scrollX: number;
967
+ colWidth: number;
968
+ treeFilehandle: import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
969
+ locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
970
+ localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
971
+ }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
659
972
  locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
660
973
  name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
661
974
  blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
@@ -663,11 +976,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
663
976
  locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
664
977
  name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
665
978
  handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
666
- }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
667
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
668
- localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
669
- }>, any>, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
670
- msaFilehandle: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").ITypeUnion<any, {
979
+ }> | {
671
980
  locationType: "UriLocation";
672
981
  uri: string;
673
982
  internetAccountId: string | undefined;
@@ -675,7 +984,11 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
675
984
  internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
676
985
  authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
677
986
  }> | undefined;
678
- } | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
987
+ } | undefined;
988
+ msaFilehandle: import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
989
+ locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
990
+ localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
991
+ }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
679
992
  locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
680
993
  name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
681
994
  blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
@@ -683,11 +996,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
683
996
  locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
684
997
  name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
685
998
  handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
686
- }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
687
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
688
- localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
689
- }>, any>, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
690
- treeMetadataFilehandle: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").ITypeUnion<any, {
999
+ }> | {
691
1000
  locationType: "UriLocation";
692
1001
  uri: string;
693
1002
  internetAccountId: string | undefined;
@@ -695,7 +1004,11 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
695
1004
  internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
696
1005
  authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
697
1006
  }> | undefined;
698
- } | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
1007
+ } | undefined;
1008
+ treeMetadataFilehandle: import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
1009
+ locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
1010
+ localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1011
+ }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
699
1012
  locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
700
1013
  name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
701
1014
  blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
@@ -703,11 +1016,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
703
1016
  locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
704
1017
  name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
705
1018
  handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
706
- }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
707
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
708
- localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
709
- }>, any>, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
710
- gffFilehandle: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").ITypeUnion<any, {
1019
+ }> | {
711
1020
  locationType: "UriLocation";
712
1021
  uri: string;
713
1022
  internetAccountId: string | undefined;
@@ -715,7 +1024,11 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
715
1024
  internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
716
1025
  authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
717
1026
  }> | undefined;
718
- } | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
1027
+ } | undefined;
1028
+ gffFilehandle: import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
1029
+ locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
1030
+ localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1031
+ }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
719
1032
  locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
720
1033
  name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
721
1034
  blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
@@ -723,34 +1036,23 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
723
1036
  locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
724
1037
  name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
725
1038
  handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
726
- }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
727
- locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
728
- localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
729
- }>, any>, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
730
- currentAlignment: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
731
- collapsed: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
732
- showOnly: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
733
- turnedOffTracks: import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
734
- data: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IModelType<{
735
- tree: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
736
- msa: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
737
- treeMetadata: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
738
- gff: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
739
- }, {
740
- setTree(tree?: string): void;
741
- setMSA(msa?: string): void;
742
- setTreeMetadata(treeMetadata?: string): void;
743
- setGFF(gff?: string): void;
744
- }, import("@jbrowse/mobx-state-tree")._NotCustomized, {
745
- tree: string | undefined;
746
- msa: string | undefined;
747
- treeMetadata: string | undefined;
748
- gff: string | undefined;
749
- }>, [undefined]>;
750
- featureFilters: import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
751
- relativeTo: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
752
- highlightColumns: import("@jbrowse/mobx-state-tree").IType<number[] | undefined, number[] | undefined, number[] | undefined>;
753
- }>, symbol> & import("@jbrowse/mobx-state-tree")._NotCustomized>;
1039
+ }> | {
1040
+ locationType: "UriLocation";
1041
+ uri: string;
1042
+ internetAccountId: string | undefined;
1043
+ internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
1044
+ internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
1045
+ authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
1046
+ }> | undefined;
1047
+ } | undefined;
1048
+ currentAlignment: number;
1049
+ collapsed: string[];
1050
+ showOnly: string | undefined;
1051
+ turnedOffTracks: import("mobx").IKeyValueMap<boolean>;
1052
+ featureFilters: import("mobx").IKeyValueMap<boolean>;
1053
+ relativeTo: string | undefined;
1054
+ highlightColumns: number[] | undefined;
1055
+ } & import("@jbrowse/mobx-state-tree")._NotCustomized>;
754
1056
  export type JBrowsePluginMsaViewStateModel = ReturnType<typeof stateModelFactory>;
755
1057
  export type JBrowsePluginMsaViewModel = Instance<JBrowsePluginMsaViewStateModel>;
756
1058
  export { type MafRegion, type MsaViewInitState } from './types';