jbrowse-plugin-msaview 5.16.2 → 5.17.0

package/dist/MsaViewPanel/model.d.ts

@@ -112,7 +112,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     displayName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     minimized: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-}, "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" | "domainFill" | "drawMsaLetters" | "embeddedMode" | "encodings" | "features" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "msaFilehandle" | "region" | "relativeTo" | "residueMappings" | "rotated" | "rowHeight" | "rowPanels" | "scrollX" | "scrollY" | "scrollZoom" | "scrollZoomAxis" | "selection" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "trackHeights" | "treeFilehandle" | "treeMetadataFilehandle" | "treeRoot" | "turnedOffFeatures" | "turnedOffTracks"> & Omit<Omit<Omit<{}, "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "treeAreaWidth" | "treeOrder" | "treeWidth"> & {
+}, "id" | "type" | "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "treeAreaWidth" | "treeOrder" | "treeWidth" | "bgColor" | "colorSchemeName" | "customColorScheme" | "msaFormat" | "showColumnStats" | "allowedGappyness" | "clades" | "cladesSeeded" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "domainFill" | "drawMsaLetters" | "embeddedMode" | "encodings" | "features" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "msaFilehandle" | "region" | "relativeTo" | "residueMappings" | "rotated" | "rowHeight" | "rowPanels" | "scrollX" | "scrollY" | "scrollZoom" | "scrollZoomAxis" | "selection" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "trackHeights" | "treeFilehandle" | "treeMetadataFilehandle" | "treeRoot" | "turnedOffFeatures" | "turnedOffTracks"> & Omit<Omit<Omit<{}, "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "treeAreaWidth" | "treeOrder" | "treeWidth"> & {
     drawLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     labelsAlignRight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     treeAreaWidth: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
@@ -129,8 +129,8 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     colorSchemeName: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     customColorScheme: import("@jbrowse/mobx-state-tree").IType<Record<string, string> | undefined, Record<string, string> | undefined, Record<string, string> | undefined>;
     showColumnStats: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-    msaFormat: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<import("react-msaview").MSAFormat>>;
-}, "id" | "type" | "allowedGappyness" | "clades" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "domainFill" | "drawMsaLetters" | "embeddedMode" | "encodings" | "features" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "msaFilehandle" | "region" | "relativeTo" | "residueMappings" | "rotated" | "rowHeight" | "rowPanels" | "scrollX" | "scrollY" | "scrollZoom" | "scrollZoomAxis" | "selection" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "trackHeights" | "treeFilehandle" | "treeMetadataFilehandle" | "treeRoot" | "turnedOffFeatures" | "turnedOffTracks"> & {
+    msaFormat: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<import("msa-parsers").MSAFormat>>;
+}, "id" | "type" | "allowedGappyness" | "clades" | "cladesSeeded" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "domainFill" | "drawMsaLetters" | "embeddedMode" | "encodings" | "features" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "msaFilehandle" | "region" | "relativeTo" | "residueMappings" | "rotated" | "rowHeight" | "rowPanels" | "scrollX" | "scrollY" | "scrollZoom" | "scrollZoomAxis" | "selection" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "trackHeights" | "treeFilehandle" | "treeMetadataFilehandle" | "treeRoot" | "turnedOffFeatures" | "turnedOffTracks"> & {
     id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     showDomains: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     domainFill: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
@@ -473,9 +473,10 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     rotated: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISimpleType<string>>, [undefined]>;
     treeRoot: import("@jbrowse/mobx-state-tree").IType<import("react-msaview").TreeRoot | undefined, import("react-msaview").TreeRoot | undefined, import("react-msaview").TreeRoot | undefined>;
     showOnly: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+    cladesSeeded: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     turnedOffTracks: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>, [undefined]>;
     trackHeights: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<number>>, [undefined]>;
-    columnTracks: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").IType<import("react-msaview").ColumnTrackSpec, import("react-msaview").ColumnTrackSpec, import("react-msaview").ColumnTrackSpec>, import("react-msaview").ColumnTrackSpec, import("@jbrowse/mobx-state-tree")._NotCustomized>>, [undefined]>;
+    columnTracks: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("react-msaview").ColumnTrackSpec, import("react-msaview").ColumnTrackSpec, import("react-msaview").ColumnTrackSpec>>, [undefined]>;
     residueMappings: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("react-msaview").ResidueMapping, import("react-msaview").ResidueMapping, import("react-msaview").ResidueMapping>>, [undefined]>;
     data: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IModelType<{
         tree: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
@@ -498,8 +499,8 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     selection: import("@jbrowse/mobx-state-tree").IType<import("react-msaview").MsaSelection | undefined, import("react-msaview").MsaSelection | undefined, import("react-msaview").MsaSelection | undefined>;
     region: import("@jbrowse/mobx-state-tree").IType<import("react-msaview").Region | undefined, import("react-msaview").Region | undefined, import("react-msaview").Region | undefined>;
     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]>;
-    encodings: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").IType<import("react-msaview").Encoding, import("react-msaview").Encoding, import("react-msaview").Encoding>, import("react-msaview").Encoding | import("react-msaview").LegacyEncoding, import("@jbrowse/mobx-state-tree")._NotCustomized>>, [undefined]>;
-    rowPanels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").IType<import("react-msaview").RowPanelSpec, import("react-msaview").RowPanelSpec, import("react-msaview").RowPanelSpec>, import("react-msaview").LegacyRowPanel | import("react-msaview").RowPanelSpec, import("@jbrowse/mobx-state-tree")._NotCustomized>>, [undefined]>;
+    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]>;
+    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]>;
 }, "init" | "querySeqName" | "embeddedMode" | "launchCompleted" | "connectedViewId" | "connectedFeature" | "connectedTranscript" | "blastParams" | "orthologParams" | "querySeqOffset" | "uniprotId" | "zoomToBaseLevel" | "dataStoreId" | "mafRegion" | "domainsOnGenome"> & {
     connectedViewId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     connectedFeature: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
@@ -554,9 +555,10 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     setCustomColorScheme(map?: Record<string, string>): void;
     setBgColor(arg: boolean): void;
     setShowColumnStats(arg: boolean): void;
-    setMSAFormat(arg?: import("react-msaview").MSAFormat): void;
+    setMSAFormat(arg?: import("msa-parsers").MSAFormat): void;
 } & {
     headerHeight: number;
+    availableHeight: number | undefined;
     settingsOpen: boolean;
     zoomHeld: {
         col: number;
@@ -592,7 +594,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     dismissedWarnings: string[];
     resetCount: number;
     hostCarriesData: boolean;
-    annotations: import("react-msaview").Annotation[];
+    annotations: import("msa-parsers").Annotation[];
 } & {
     drawRelativeTo(id: string | undefined): void;
     setHideGaps(arg: boolean): void;
@@ -603,6 +605,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     setSettingsOpen(arg: boolean): void;
     setHighResScaleFactor(arg: number): void;
     setHeight(height: number): void;
+    setAvailableHeight(height?: number): void;
     setError(error?: unknown): void;
     addWarning(warning: string): void;
     setHostCarriesData(arg: boolean): void;
@@ -628,6 +631,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     toggleCollapsed(node: string): void;
     toggleRotated(node: string): void;
     clearRotated(): void;
+    clearNodeState(): void;
     setTreeRoot(treeRoot?: import("react-msaview").TreeRoot): void;
     setShowOnly(node?: string): void;
     setData(data: {
@@ -672,8 +676,8 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     readonly rowData: Record<string, Record<string, string> | undefined>;
     rowDataOf(name: string): Record<string, string> | undefined;
     readonly rowFields: string[];
-    readonly MSA: import("react-msaview").MSAParserType | null;
-    readonly allAnnotations: import("react-msaview").Annotation[];
+    readonly MSA: import("msa-parsers").MSAParserType | null;
+    readonly allAnnotations: import("msa-parsers").Annotation[];
     readonly actuallyShowDomains: boolean;
     readonly numColumns: number;
     readonly inputTree: import("react-msaview").NodeWithIds;
@@ -687,9 +691,11 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
         names: string[];
         depth: number;
     };
+    readonly treeHierarchy: import("react-msaview").HierarchyNode<import("react-msaview").NodeWithIds>;
     readonly maxTipLabelWidth: number;
     readonly labelColumnWidth: number;
     readonly fittedTreeAreaWidth: number;
+    readonly effectiveHeight: number;
     readonly effectiveTreeAreaWidth: number;
     readonly effectiveTreeWidth: number;
     readonly showTreeText: boolean;
@@ -807,12 +813,12 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     readonly topBandHeight: number;
     readonly msaAreaHeight: number;
     readonly totalTrackAreaHeight: number;
-    readonly annotationTypes: Map<string, import("react-msaview").Annotation>;
+    readonly annotationTypes: Map<string, import("msa-parsers").Annotation>;
     readonly defaultOffAccessions: Set<string>;
     featureOff(accession: string): boolean;
-    readonly filteredAnnotations: import("react-msaview").Annotation[];
+    readonly filteredAnnotations: import("msa-parsers").Annotation[];
     readonly cellFill: "residue" | "domain" | "none";
-    readonly annotationsByRow: Record<string, import("react-msaview").Annotation[]>;
+    readonly annotationsByRow: Record<string, import("msa-parsers").Annotation[]>;
 } & {
     readonly showVerticalScrollbar: boolean;
 } & {
@@ -838,6 +844,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     setHoveredTreeNode(nodeId?: string): void;
     calculateNeighborJoiningTreeFromMSA(): void;
     rerootAt(nodeId: string): void;
+    seedCladeMarks(): void;
     replaceTree(newick: string): void;
     resetZoom(): void;
     zoomAtCenter(scaleFactor: number, axis?: "both" | "horizontal" | "vertical"): void;
@@ -848,14 +855,14 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     endWheelZoom(): void;
     doScrollY(deltaY: number): void;
     setScrollY(n: number): void;
-    setAnnotations(annotations: import("react-msaview").Annotation[]): void;
+    setAnnotations(annotations: import("msa-parsers").Annotation[]): void;
     applyGFFText(gffText: string): void;
     doScrollX(deltaX: number): void;
     setScrollX(n: number): void;
-    setColumnTracks(tracks: (import("react-msaview").ColumnTrackSpec | import("react-msaview").LegacyColumnTrack)[]): void;
+    setColumnTracks(tracks: import("react-msaview").ColumnTrackSpec[]): void;
     setRowData(rowData: import("react-msaview").RowDataInput): void;
-    setEncodings(encodings: (import("react-msaview").Encoding | import("react-msaview").LegacyEncoding)[]): void;
-    setRowPanels(panels: (import("react-msaview").RowPanelSpec | import("react-msaview").LegacyRowPanel)[]): void;
+    setEncodings(encodings: import("react-msaview").Encoding[]): void;
+    setRowPanels(panels: import("react-msaview").RowPanelSpec[]): void;
     setResidueMappings(mappings: import("react-msaview").ResidueMapping[]): void;
     toggleTrack(id: string): void;
     setTracksShown(ids: string[], shown: boolean): void;
@@ -868,24 +875,25 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     readonly hoveredCell: import("react-msaview").Cell | undefined;
     readonly clickedCell: import("react-msaview").Cell | undefined;
     readonly viewport: import("react-msaview").Viewport | undefined;
-    readonly segmentDomainTypes: import("react-msaview").Annotation[];
-    readonly categoricalDomainTypes: import("react-msaview").Annotation[];
+    readonly segmentDomainTypes: import("msa-parsers").Annotation[];
+    readonly domainLegendEntries: import("react-msaview").LegendEntry[];
+    readonly categoricalDomainTypes: import("msa-parsers").Annotation[];
     readonly fillPalette: {
         [x: string]: string;
     };
     readonly featureFillEncoding: import("react-msaview").ResolvedEncoding | undefined;
-    readonly featureColors: Map<import("react-msaview").Annotation, {
+    readonly featureColors: Map<import("msa-parsers").Annotation, {
         fill: string;
         stroke: string;
     }>;
-    readonly featureLabels: Map<import("react-msaview").Annotation, string> | undefined;
+    readonly featureLabels: Map<import("msa-parsers").Annotation, string> | undefined;
     readonly segmentLabels: Map<string, string>;
-    readonly visibleDomainTypes: import("react-msaview").Annotation[];
+    readonly visibleDomainTypes: import("msa-parsers").Annotation[];
     readonly legends: import("react-msaview").Legend[];
     readonly domainUnderline: boolean;
     readonly domainBands: Map<string, import("react-msaview").DomainBand[]>;
     readonly domainBandsByStart: Map<string, import("react-msaview").DomainBand[]>;
-    readonly mouseOverDomains: import("react-msaview").Annotation[];
+    readonly mouseOverDomains: import("msa-parsers").Annotation[];
     readonly referenceRowIndex: number | undefined;
     readonly hoveredRowIndices: number[];
     readonly highlightedColumnRuns: {
@@ -914,14 +922,16 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
         rowData: Record<string, string> | undefined;
     };
     readonly resolvedEncodings: import("react-msaview").ResolvedEncoding[];
+    readonly colorEncodings: import("react-msaview").ColorEncoding[];
+    encodingFor(channel: import("react-msaview").ColorEncodingChannel): import("react-msaview").ResolvedEncoding | undefined;
     readonly resolvedScales: Map<string, import("react-msaview").SharedScale>;
     scaleOf(channel: import("react-msaview").ColorChannel, table: import("react-msaview").ScaleTable): import("react-msaview").SharedScale;
     readonly rowPanelScales: ({
         header: string;
         field: string;
         kind: "strip";
-        legend: import("react-msaview").LegendEntry[];
         colors: Map<string, string>;
+        legend: import("react-msaview").LegendEntry[];
         legendKey?: string | undefined;
         legendTitle?: string | undefined;
     } | {
@@ -929,14 +939,14 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
         x: "column" | "position";
         field?: string | undefined;
         kind: "features";
-        legend: import("react-msaview").LegendEntry[];
-        colors: Map<import("react-msaview").Annotation, {
+        colors: Map<import("msa-parsers").Annotation, {
             fill: string;
             stroke: string;
         }>;
+        legend: import("react-msaview").LegendEntry[];
         legendKey?: string | undefined;
         legendTitle?: string | undefined;
-        labels?: Map<import("react-msaview").Annotation, string> | undefined;
+        labels?: Map<import("msa-parsers").Annotation, string> | undefined;
     })[];
     readonly resolvedRowPanels: import("react-msaview").ResolvedRowPanel[];
     readonly featureAlignShifts: Map<string, Map<string, number>>;
@@ -1327,7 +1337,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     displayName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     minimized: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-}, "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" | "domainFill" | "drawMsaLetters" | "embeddedMode" | "encodings" | "features" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "msaFilehandle" | "region" | "relativeTo" | "residueMappings" | "rotated" | "rowHeight" | "rowPanels" | "scrollX" | "scrollY" | "scrollZoom" | "scrollZoomAxis" | "selection" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "trackHeights" | "treeFilehandle" | "treeMetadataFilehandle" | "treeRoot" | "turnedOffFeatures" | "turnedOffTracks"> & Omit<Omit<Omit<{}, "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "treeAreaWidth" | "treeOrder" | "treeWidth"> & {
+}, "id" | "type" | "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "treeAreaWidth" | "treeOrder" | "treeWidth" | "bgColor" | "colorSchemeName" | "customColorScheme" | "msaFormat" | "showColumnStats" | "allowedGappyness" | "clades" | "cladesSeeded" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "domainFill" | "drawMsaLetters" | "embeddedMode" | "encodings" | "features" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "msaFilehandle" | "region" | "relativeTo" | "residueMappings" | "rotated" | "rowHeight" | "rowPanels" | "scrollX" | "scrollY" | "scrollZoom" | "scrollZoomAxis" | "selection" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "trackHeights" | "treeFilehandle" | "treeMetadataFilehandle" | "treeRoot" | "turnedOffFeatures" | "turnedOffTracks"> & Omit<Omit<Omit<{}, "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "treeAreaWidth" | "treeOrder" | "treeWidth"> & {
     drawLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     labelsAlignRight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     treeAreaWidth: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
@@ -1344,8 +1354,8 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     colorSchemeName: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     customColorScheme: import("@jbrowse/mobx-state-tree").IType<Record<string, string> | undefined, Record<string, string> | undefined, Record<string, string> | undefined>;
     showColumnStats: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-    msaFormat: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<import("react-msaview").MSAFormat>>;
-}, "id" | "type" | "allowedGappyness" | "clades" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "domainFill" | "drawMsaLetters" | "embeddedMode" | "encodings" | "features" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "msaFilehandle" | "region" | "relativeTo" | "residueMappings" | "rotated" | "rowHeight" | "rowPanels" | "scrollX" | "scrollY" | "scrollZoom" | "scrollZoomAxis" | "selection" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "trackHeights" | "treeFilehandle" | "treeMetadataFilehandle" | "treeRoot" | "turnedOffFeatures" | "turnedOffTracks"> & {
+    msaFormat: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<import("msa-parsers").MSAFormat>>;
+}, "id" | "type" | "allowedGappyness" | "clades" | "cladesSeeded" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "domainFill" | "drawMsaLetters" | "embeddedMode" | "encodings" | "features" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "msaFilehandle" | "region" | "relativeTo" | "residueMappings" | "rotated" | "rowHeight" | "rowPanels" | "scrollX" | "scrollY" | "scrollZoom" | "scrollZoomAxis" | "selection" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "trackHeights" | "treeFilehandle" | "treeMetadataFilehandle" | "treeRoot" | "turnedOffFeatures" | "turnedOffTracks"> & {
     id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     showDomains: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     domainFill: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
@@ -1688,9 +1698,10 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     rotated: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISimpleType<string>>, [undefined]>;
     treeRoot: import("@jbrowse/mobx-state-tree").IType<import("react-msaview").TreeRoot | undefined, import("react-msaview").TreeRoot | undefined, import("react-msaview").TreeRoot | undefined>;
     showOnly: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+    cladesSeeded: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     turnedOffTracks: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>, [undefined]>;
     trackHeights: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<number>>, [undefined]>;
-    columnTracks: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").IType<import("react-msaview").ColumnTrackSpec, import("react-msaview").ColumnTrackSpec, import("react-msaview").ColumnTrackSpec>, import("react-msaview").ColumnTrackSpec, import("@jbrowse/mobx-state-tree")._NotCustomized>>, [undefined]>;
+    columnTracks: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("react-msaview").ColumnTrackSpec, import("react-msaview").ColumnTrackSpec, import("react-msaview").ColumnTrackSpec>>, [undefined]>;
     residueMappings: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("react-msaview").ResidueMapping, import("react-msaview").ResidueMapping, import("react-msaview").ResidueMapping>>, [undefined]>;
     data: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IModelType<{
         tree: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
@@ -1713,8 +1724,8 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     selection: import("@jbrowse/mobx-state-tree").IType<import("react-msaview").MsaSelection | undefined, import("react-msaview").MsaSelection | undefined, import("react-msaview").MsaSelection | undefined>;
     region: import("@jbrowse/mobx-state-tree").IType<import("react-msaview").Region | undefined, import("react-msaview").Region | undefined, import("react-msaview").Region | undefined>;
     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]>;
-    encodings: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").IType<import("react-msaview").Encoding, import("react-msaview").Encoding, import("react-msaview").Encoding>, import("react-msaview").Encoding | import("react-msaview").LegacyEncoding, import("@jbrowse/mobx-state-tree")._NotCustomized>>, [undefined]>;
-    rowPanels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").IType<import("react-msaview").RowPanelSpec, import("react-msaview").RowPanelSpec, import("react-msaview").RowPanelSpec>, import("react-msaview").LegacyRowPanel | import("react-msaview").RowPanelSpec, import("@jbrowse/mobx-state-tree")._NotCustomized>>, [undefined]>;
+    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]>;
+    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]>;
 }, "init" | "querySeqName" | "embeddedMode" | "launchCompleted" | "connectedViewId" | "connectedFeature" | "connectedTranscript" | "blastParams" | "orthologParams" | "querySeqOffset" | "uniprotId" | "zoomToBaseLevel" | "dataStoreId" | "mafRegion" | "domainsOnGenome"> & {
     connectedViewId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     connectedFeature: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
@@ -1731,12 +1742,12 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     mafRegion: import("@jbrowse/mobx-state-tree").IType<MafRegion | undefined, MafRegion | undefined, MafRegion | undefined>;
     embeddedMode: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     domainsOnGenome: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-}>, "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" | "domainFill" | "drawMsaLetters" | "embeddedMode" | "encodings" | "features" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "msaFilehandle" | "region" | "relativeTo" | "residueMappings" | "rotated" | "rowHeight" | "rowPanels" | "scrollX" | "scrollY" | "scrollZoom" | "scrollZoomAxis" | "selection" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "trackHeights" | "treeFilehandle" | "treeMetadataFilehandle" | "treeRoot" | "turnedOffFeatures" | "turnedOffTracks"> & ({
+}>, "id" | "type" | "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "treeAreaWidth" | "treeOrder" | "treeWidth" | "bgColor" | "colorSchemeName" | "customColorScheme" | "msaFormat" | "showColumnStats" | "allowedGappyness" | "clades" | "cladesSeeded" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "domainFill" | "drawMsaLetters" | "embeddedMode" | "encodings" | "features" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "msaFilehandle" | "region" | "relativeTo" | "residueMappings" | "rotated" | "rowHeight" | "rowPanels" | "scrollX" | "scrollY" | "scrollZoom" | "scrollZoomAxis" | "selection" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "trackHeights" | "treeFilehandle" | "treeMetadataFilehandle" | "treeRoot" | "turnedOffFeatures" | "turnedOffTracks"> & ({
     bgColor: boolean;
     colorSchemeName: string;
     customColorScheme: Record<string, string> | undefined;
     showColumnStats: boolean;
-    msaFormat: import("react-msaview").MSAFormat | undefined;
+    msaFormat: import("msa-parsers").MSAFormat | undefined;
     drawLabels: boolean;
     labelsAlignRight: boolean;
     treeAreaWidth: number | undefined;
@@ -1851,6 +1862,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     rotated: string[];
     treeRoot: import("react-msaview").TreeRoot | undefined;
     showOnly: string | undefined;
+    cladesSeeded: boolean;
     turnedOffTracks: import("mobx").IKeyValueMap<boolean>;
     trackHeights: import("mobx").IKeyValueMap<number>;
     residueMappings: import("react-msaview").ResidueMapping[];
@@ -1875,7 +1887,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     colorSchemeName: string;
     customColorScheme: Record<string, string> | undefined;
     showColumnStats: boolean;
-    msaFormat: import("react-msaview").MSAFormat | undefined;
+    msaFormat: import("msa-parsers").MSAFormat | undefined;
     drawLabels: boolean;
     labelsAlignRight: boolean;
     treeAreaWidth: number | undefined;
@@ -1990,6 +2002,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     rotated: string[];
     treeRoot: import("react-msaview").TreeRoot | undefined;
     showOnly: string | undefined;
+    cladesSeeded: boolean;
     turnedOffTracks: import("mobx").IKeyValueMap<boolean>;
     trackHeights: import("mobx").IKeyValueMap<number>;
     residueMappings: import("react-msaview").ResidueMapping[];

package/dist/MsaViewPanel/storedData.test.js

@@ -69,7 +69,7 @@ describe('what a reload would lose', () => {
     });
     test('a url-loaded alignment is not, but a large local GFF on it is', () => {
         const model = view({ msaFilehandle: URL_MSA });
-        model.setMSA(BIG_MSA);
+        model.data.setMSA(BIG_MSA);
         model.setGFF(BIG_GFF);
         expect(model.unsavedDocuments).toEqual({
             msa: undefined,
@@ -87,7 +87,7 @@ describe('what a reload would lose', () => {
     });
     test('a GFF read from a url is not', () => {
         const model = view({ gffFilehandle: URL_GFF });
-        model.setGFF(BIG_GFF);
+        model.data.setGFF(BIG_GFF);
         expect(model.unsavedDocuments.gff).toBeUndefined();
     });
 });
@@ -187,7 +187,7 @@ describe('a row two views name', () => {
         await settle();
         expect(copy.data.gff).toBe(BIG_GFF);
         copy.setGFFFilehandle(URL_GFF);
-        copy.setGFF('a\t.\tdomain\t1\t2');
+        copy.data.setGFF('a\t.\tdomain\t1\t2');
         await settle();
         await settle();
         expect(rows.get('shared')).toEqual({ gff: BIG_GFF });
@@ -246,7 +246,7 @@ describe('keeping IndexedDB up to date', () => {
     });
     test('a large local GFF on a url-loaded view is written, and only it', async () => {
         const model = view({ msaFilehandle: URL_MSA });
-        model.setMSA(BIG_MSA);
+        model.data.setMSA(BIG_MSA);
         model.setGFF(BIG_GFF);
         await settle();
         expect(mockStore).toHaveBeenCalledTimes(1);

package/dist/chunks/{AboutDialog-UIDZTTTE.js → AboutDialog-CFANNPHL.js}

@@ -1,2 +1,2 @@
-import{a as n}from"./chunk-TVOPZHTJ.js";import{a as l}from"./chunk-YOLY6H5C.js";import{S as r,n as o,u as t}from"./chunk-EXFKF6XR.js";import{r as e}from"./chunk-TEYYBCMF.js";import"./chunk-KVMUXFPB.js";function i({onClose:a}){return e.createElement(l,{open:!0,title:"About",onClose:()=>{a()}},e.createElement(o,null,e.createElement(r,null,"MSAView ",n," (",e.createElement(t,{target:"_blank",rel:"noopener",href:"https://github.com/gmod/react-msaview"},"Github"),")"),e.createElement("ul",null,e.createElement("li",null,e.createElement(r,null,"We use some color schemes from the"," ",e.createElement(t,{target:"_blank",rel:"noopener",href:"https://github.com/biotite-dev/biotite"},"biotite")," ","project, and their license is reproduced"," ",e.createElement(t,{target:"_blank",rel:"noopener",href:"https://github.com/biotite-dev/biotite/blob/master/LICENSE.rst"},"here"))),e.createElement("li",null,e.createElement(r,null,"See this page for some information on jalview colorings"," ",e.createElement(t,{target:"_blank",rel:"noopener",href:"https://www.jalview.org/help/html/colourSchemes/"},"here"))),e.createElement("li",null,e.createElement(r,null,"See this page for some info on the clustal, cinema, maeditor, and lesk color schemes"," ",e.createElement(t,{target:"_blank",rel:"noopener",href:"http://www.bioinformatics.nl/~berndb/aacolour.html"},"here"))),e.createElement("li",null,e.createElement(r,null,"See this paper about the flower color scheme"," ",e.createElement(t,{target:"_blank",rel:"noopener",href:"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7245768/"},"here"))))))}export{i as default};
-//# sourceMappingURL=AboutDialog-UIDZTTTE.js.map
+import{a as n}from"./chunk-FDAPTOY5.js";import{a as l}from"./chunk-YOLY6H5C.js";import{S as r,n as o,u as t}from"./chunk-EXFKF6XR.js";import{r as e}from"./chunk-TEYYBCMF.js";import"./chunk-KVMUXFPB.js";function i({onClose:a}){return e.createElement(l,{open:!0,title:"About",onClose:()=>{a()}},e.createElement(o,null,e.createElement(r,null,"MSAView ",n," (",e.createElement(t,{target:"_blank",rel:"noopener",href:"https://github.com/gmod/react-msaview"},"Github"),")"),e.createElement("ul",null,e.createElement("li",null,e.createElement(r,null,"We use some color schemes from the"," ",e.createElement(t,{target:"_blank",rel:"noopener",href:"https://github.com/biotite-dev/biotite"},"biotite")," ","project, and their license is reproduced"," ",e.createElement(t,{target:"_blank",rel:"noopener",href:"https://github.com/biotite-dev/biotite/blob/master/LICENSE.rst"},"here"))),e.createElement("li",null,e.createElement(r,null,"See this page for some information on jalview colorings"," ",e.createElement(t,{target:"_blank",rel:"noopener",href:"https://www.jalview.org/help/html/colourSchemes/"},"here"))),e.createElement("li",null,e.createElement(r,null,"See this page for some info on the clustal, cinema, maeditor, and lesk color schemes"," ",e.createElement(t,{target:"_blank",rel:"noopener",href:"http://www.bioinformatics.nl/~berndb/aacolour.html"},"here"))),e.createElement("li",null,e.createElement(r,null,"See this paper about the flower color scheme"," ",e.createElement(t,{target:"_blank",rel:"noopener",href:"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7245768/"},"here"))))))}export{i as default};
+//# sourceMappingURL=AboutDialog-CFANNPHL.js.map

package/dist/chunks/{AboutDialog-UIDZTTTE.js.map → AboutDialog-CFANNPHL.js.map}

@@ -1,6 +1,6 @@
 {
   "version": 3,
-  "sources": ["../../node_modules/.pnpm/react-msaview@9.8.0_4d87629ce60f4a70309a0d727f3e914b/node_modules/react-msaview/src/components/dialogs/AboutDialog.tsx"],
+  "sources": ["../../node_modules/.pnpm/react-msaview@10.0.0_4d87629ce60f4a70309a0d727f3e914b/node_modules/react-msaview/src/components/dialogs/AboutDialog.tsx"],
   "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"],
   "mappings": "0MAOc,SAAPA,EAA6B,CAAE,QAAAC,CAAO,EAA2B,CACtE,OACEC,EAAA,cAACC,EAAM,CACL,KAAI,GACJ,MAAM,QACN,QAAS,IAAK,CACZF,EAAO,CACT,CAAC,EAEDC,EAAA,cAACE,EAAa,KACZF,EAAA,cAACG,EAAU,gBACAC,OACTJ,EAAA,cAACK,EAAI,CACH,OAAO,SACP,IAAI,WACJ,KAAK,uCAAuC,EAAA,QAAA,OAOhDL,EAAA,cAAA,KAAA,KACEA,EAAA,cAAA,KAAA,KACEA,EAAA,cAACG,EAAU,0CAC0B,IACnCH,EAAA,cAACK,EAAI,CACH,OAAO,SACP,IAAI,WACJ,KAAK,wCAAwC,EAAA,SAAA,EAGvC,+CACiC,IACzCL,EAAA,cAACK,EAAI,CACH,OAAO,SACP,IAAI,WACJ,KAAK,gEAAgE,EAAA,MAAA,CAGhE,CACI,EAEfL,EAAA,cAAA,KAAA,KACEA,EAAA,cAACG,EAAU,+DAC+C,IACxDH,EAAA,cAACK,EAAI,CACH,OAAO,SACP,IAAI,WACJ,KAAK,kDAAkD,EAAA,MAAA,CAGlD,CACI,EAEfL,EAAA,cAAA,KAAA,KACEA,EAAA,cAACG,EAAU,4FAEU,IACnBH,EAAA,cAACK,EAAI,CACH,OAAO,SACP,IAAI,WACJ,KAAK,oDAAoD,EAAA,MAAA,CAGpD,CACI,EAEfL,EAAA,cAAA,KAAA,KACEA,EAAA,cAACG,EAAU,oDACoC,IAC7CH,EAAA,cAACK,EAAI,CACH,OAAO,SACP,IAAI,WACJ,KAAK,uDAAuD,EAAA,MAAA,CAGvD,CACI,CACV,CACF,CACS,CAGtB",
   "names": ["AboutDialog", "onClose", "react_default", "Dialog", "DialogContent", "Typography", "version", "Link"]

package/dist/chunks/AnnotationFileDialog-27HTSCJC.js

@@ -0,0 +1,2 @@
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+//# sourceMappingURL=AnnotationFileDialog-27HTSCJC.js.map

package/dist/chunks/{AnnotationFileDialog-TFIHQACD.js.map → AnnotationFileDialog-27HTSCJC.js.map}

@@ -1,7 +1,7 @@
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-  "sources": ["../../node_modules/.pnpm/react-msaview@9.8.0_4d87629ce60f4a70309a0d727f3e914b/node_modules/react-msaview/src/components/dialogs/AnnotationFileDialog.tsx"],
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A\n                // filehandle left set would make the snapshot drop that text\n                model.setGFFFilehandle(undefined)\n                model.setGFF(annotationTextToGFF(text))\n                model.setShowDomains(true)\n                model.setCellFill('domain')\n                handleClose()\n              } catch (e) {\n                console.error(e)\n                setError(e)\n              } finally {\n                setLoading(false)\n              }\n            })()\n          }}\n        >\n          Open annotations\n        </Button>\n        <Button\n          variant=\"contained\"\n          color=\"secondary\"\n          onClick={() => {\n            handleClose()\n          }}\n        >\n          Cancel\n        </Button>\n      </DialogActions>\n    </Dialog>\n  )\n})\n\nexport default AnnotationFileDialog\n"],
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+  "sources": ["../../node_modules/.pnpm/react-msaview@10.0.0_4d87629ce60f4a70309a0d727f3e914b/node_modules/react-msaview/src/components/dialogs/AnnotationFileDialog.tsx"],
+  "sourcesContent": ["import React, { useState } from 'react'\n\nimport { Dialog, ErrorMessage } from '@jbrowse/core/ui'\nimport {\n  Button,\n  DialogActions,\n  DialogContent,\n  FormControl,\n  FormControlLabel,\n  Link,\n  Radio,\n  RadioGroup,\n  TextField,\n  Typography,\n} from '@mui/material'\nimport { observer } from 'mobx-react'\nimport { annotationTextToGFF } from 'msa-parsers'\n\nimport type { MsaViewModel } from '../../model.ts'\n\nconst domainsTutorial = 'https://gmod.org/JBrowseMSA/tutorials/protein_family'\n\nasync function fetchText(url: string) {\n  const response = await fetch(url)\n  if (!response.ok) {\n    throw new Error(\n      `HTTP ${response.status} fetching ${url} ${await response.text()}`,\n    )\n  }\n  return response.text()\n}\n\nconst AnnotationFileDialog = observer(function ({\n  handleClose,\n  model,\n}: {\n  handleClose: () => void\n  model: MsaViewModel\n}) {\n  const [file, setFile] = useState<File>()\n  const [choice, setChoice] = useState('file')\n  const [url, setUrl] = useState('')\n  const [error, setError] = useState<unknown>()\n  const [loading, setLoading] = useState(false)\n\n  // the error is shown here rather than notified: the standalone app and the\n  // MSAViewer component have no jbrowse session to notify, and asking one for\n  // its notify() threw out of the success path into the catch, which threw\n  // again on the same missing session\n  return (\n    <Dialog\n      maxWidth=\"xl\"\n      title=\"Open annotation file\"\n      onClose={() => {\n        handleClose()\n      }}\n      open\n    >\n      <DialogContent>\n        {error ? <ErrorMessage error={error} /> : null}\n        <Typography>\n          Open a GFF3 file of annotations, such as the one `react-msaview-cli\n          interpro` writes, or the JSON an InterProScan run returns.{' '}\n          <Link\n            href={domainsTutorial}\n            target=\"_blank\"\n            rel=\"noopener noreferrer\"\n          >\n            How to make one\n          </Link>\n        </Typography>\n\n        <div style={{ display: 'flex', margin: 30 }}>\n          <FormControl component=\"fieldset\">\n            <RadioGroup\n              value={choice}\n              onChange={event => {\n                setChoice(event.target.value)\n              }}\n            >\n              <FormControlLabel value=\"url\" control={<Radio />} label=\"URL\" />\n              <FormControlLabel value=\"file\" control={<Radio />} label=\"File\" />\n            </RadioGroup>\n          </FormControl>\n          {choice === 'url' ? 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 }

package/dist/chunks/{ExportSVGDialog-AYE4AXS3.js → ExportSVGDialog-P4ICAFJQ.js}

@@ -1,2 +1,2 @@
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+import{a as E}from"./chunk-LGW6EKNG.js";import{aa as L,ba as D}from"./chunk-7FQ6JH7S.js";import{a as k,b as C}from"./chunk-YOLY6H5C.js";import{a as y}from"./chunk-PFO3G4CM.js";import{D as p,E as F,S as G,T as I,d as T,g as m,j as b,m as w,n as M,q as S,r as u,s as A}from"./chunk-EXFKF6XR.js";import{p as r,r as e}from"./chunk-TEYYBCMF.js";import"./chunk-KVMUXFPB.js";function H(t){requestAnimationFrame(()=>{requestAnimationFrame(t)})}var J=y(function({model:t,onClose:l}){let[i,V]=r(!0),[n,z]=r(!0),[o,P]=r("viewport"),[h,R]=r(),[c,d]=r(!1),g=I(),{turnedOnTracks:q,numColumns:B,leaves:O,showMsaLetters:_}=t,x=q.length>0,f=D(t,L(t,{theme:g,exportType:"entire",includeTracks:n})),v=_&&o==="entire"?B*O.length:0,j=v>1e5;return e.createElement(k,{onClose:()=>{l()},open:!0,title:"Export SVG"},e.createElement(M,null,h?e.createElement(C,{error:h}):null,e.createElement(G,null,"Settings:"),e.createElement(E,{label:"Include minimap?",disabled:o==="entire",checked:i,onChange:()=>{V(!i)}}),x?e.createElement(E,{label:"Include tracks?",checked:n,onChange:()=>{z(!n)}}):null,e.createElement("div",null,e.createElement(S,null,e.createElement(A,null,"Export type"),e.createElement(F,{value:o,onChange:a=>{let{value:s}=a.target;(s==="entire"||s==="viewport")&&P(s)}},e.createElement(u,{value:"entire",control:e.createElement(p,null),label:"Entire MSA"}),e.createElement(u,{value:"viewport",control:e.createElement(p,null),label:"Current viewport only"})))),j?e.createElement(T,{severity:"warning",style:{marginTop:8}},"The entire MSA is ",Math.round(f.width),"x",Math.round(f.height)," pixels and draws"," ",Math.round(v/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),e.createElement(w,null,e.createElement(m,{variant:"contained",color:"primary",disabled:c,startIcon:c?e.createElement(b,{size:16,color:"inherit"}):null,onClick:()=>{d(!0),H(()=>{t.exportSVG({theme:g,includeMinimap:i,includeTracks:x&&n,exportType:o}).then(()=>{l()}).catch(a=>{console.error(a),R(a)}).finally(()=>{d(!1)})})}},c?"Exporting\u2026":"Export"),e.createElement(m,{variant:"contained",color:"secondary",onClick:()=>{l()}},"Cancel")))}),Y=J;export{Y as default};
+//# sourceMappingURL=ExportSVGDialog-P4ICAFJQ.js.map

package/dist/chunks/{ExportSVGDialog-AYE4AXS3.js.map → ExportSVGDialog-P4ICAFJQ.js.map}

@@ -1,6 +1,6 @@
 {
   "version": 3,
-  "sources": ["../../node_modules/.pnpm/react-msaview@9.8.0_4d87629ce60f4a70309a0d727f3e914b/node_modules/react-msaview/src/components/dialogs/ExportSVGDialog.tsx"],
+  "sources": ["../../node_modules/.pnpm/react-msaview@10.0.0_4d87629ce60f4a70309a0d727f3e914b/node_modules/react-msaview/src/components/dialogs/ExportSVGDialog.tsx"],
   "sourcesContent": ["import React, { useState } from 'react'\n\nimport { Dialog, ErrorMessage } from '@jbrowse/core/ui'\nimport {\n  Alert,\n  Button,\n  CircularProgress,\n  DialogActions,\n  DialogContent,\n  FormControl,\n  FormControlLabel,\n  FormLabel,\n  Radio,\n  RadioGroup,\n  Typography,\n  useTheme,\n} from '@mui/material'\nimport { observer } from 'mobx-react'\n\nimport { exportPageSize, getLayout } from '../../exportLayout.ts'\nimport Checkbox2 from '../Checkbox2.tsx'\n\nimport type { MsaViewModel } from '../../model.ts'\n\n// Run after the browser has painted. A requestAnimationFrame callback still\n// runs *before* the frame it was queued for, so one alone hands the main thread\n// to the render with the spinner not yet on screen; the second fires once that\n// frame is out.\nfunction afterPaint(fn: () => void) {\n  requestAnimationFrame(() => {\n    requestAnimationFrame(fn)\n  })\n}\n\nconst ExportSVGDialog = observer(function ({\n  model,\n  onClose,\n}: {\n  model: MsaViewModel\n  onClose: () => void\n}) {\n  const [includeMinimap, setIncludeMinimap] = useState(true)\n  const [includeTracks, setIncludeTracks] = useState(true)\n  const [exportType, setExportType] = useState<'entire' | 'viewport'>(\n    'viewport',\n  )\n  const [error, setError] = useState<unknown>()\n  const [exporting, setExporting] = useState(false)\n  const theme = useTheme()\n  const { turnedOnTracks, numColumns, leaves, showMsaLetters } = model\n  const hasTracks = turnedOnTracks.length > 0\n  const entire = exportPageSize(\n    model,\n    getLayout(model, { theme, exportType: 'entire', includeTracks }),\n  )\n  // the background is one raster image whatever its size, so what the figure\n  // actually costs is its residue letters: each is an svg element of its own.\n  // Past roughly this many the export runs to tens of seconds and can exhaust\n  // the tab's memory outright\n  const glyphs =\n    showMsaLetters && exportType === 'entire' ? numColumns * leaves.length : 0\n  const isLargeExport = glyphs > 100_000\n  return (\n    <Dialog\n      onClose={() => {\n        onClose()\n      }}\n      open\n      title=\"Export SVG\"\n    >\n      <DialogContent>\n        {error ? <ErrorMessage error={error} /> : null}\n        <Typography>Settings:</Typography>\n        <Checkbox2\n          label=\"Include minimap?\"\n          disabled={exportType === 'entire'}\n          checked={includeMinimap}\n          onChange={() => {\n            setIncludeMinimap(!includeMinimap)\n          }}\n        />\n        {hasTracks ? (\n          <Checkbox2\n            label=\"Include tracks?\"\n            checked={includeTracks}\n            onChange={() => {\n              setIncludeTracks(!includeTracks)\n            }}\n          />\n        ) : null}\n        <div>\n          <FormControl>\n            <FormLabel>Export type</FormLabel>\n            <RadioGroup\n              value={exportType}\n              onChange={event => {\n                const { value } = event.target\n                if (value === 'entire' || value === 'viewport') {\n                  setExportType(value)\n                }\n              }}\n            >\n              <FormControlLabel\n                value=\"entire\"\n                control={<Radio />}\n                label=\"Entire MSA\"\n              />\n              <FormControlLabel\n                value=\"viewport\"\n                control={<Radio />}\n                label=\"Current viewport only\"\n              />\n            </RadioGroup>\n          </FormControl>\n        </div>\n        {isLargeExport ? (\n          <Alert severity=\"warning\" style={{ marginTop: 8 }}>\n            The entire MSA is {Math.round(entire.width)}x\n            {Math.round(entire.height)} pixels and draws{' '}\n            {Math.round(glyphs / 1000)}k residue letters, each its own SVG\n            element. Export may be slow or fail \u2014 zooming out far enough to hide\n            the letters exports the same alignment as an image instead.\n          </Alert>\n        ) : null}\n      </DialogContent>\n      <DialogActions>\n        <Button\n          variant=\"contained\"\n          color=\"primary\"\n          // rendering runs on the main thread and a large figure holds it for\n          // seconds; without this the button stays live through the freeze and\n          // a second click starts a second export\n          disabled={exporting}\n          startIcon={\n            exporting ? <CircularProgress size={16} color=\"inherit\" /> : null\n          }\n          onClick={() => {\n            setExporting(true)\n            afterPaint(() => {\n              void model\n                .exportSVG({\n                  theme,\n                  includeMinimap,\n                  includeTracks: hasTracks && includeTracks,\n                  exportType,\n                })\n                .then(() => {\n                  onClose()\n                })\n                .catch((e: unknown) => {\n                  console.error(e)\n                  setError(e)\n                })\n                .finally(() => {\n                  setExporting(false)\n                })\n            })\n          }}\n        >\n          {exporting ? 'Exporting\u2026' : 'Export'}\n        </Button>\n        <Button\n          variant=\"contained\"\n          color=\"secondary\"\n          onClick={() => {\n            onClose()\n          }}\n        >\n          Cancel\n        </Button>\n      </DialogActions>\n    </Dialog>\n  )\n})\n\nexport default ExportSVGDialog\n"],
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   "names": ["afterPaint", "fn", "ExportSVGDialog", "observer", "model", "onClose", "includeMinimap", "setIncludeMinimap", "useState", "includeTracks", "setIncludeTracks", "exportType", "setExportType", "error", "setError", "exporting", "setExporting", "theme", "useTheme", "turnedOnTracks", "numColumns", "leaves", "showMsaLetters", "hasTracks", "entire", "exportPageSize", "getLayout", "glyphs", "isLargeExport", "react_default", "Dialog", "DialogContent", "ErrorMessage", "Typography", "Checkbox2", "FormControl", "FormLabel", "RadioGroup", "event", "value", "FormControlLabel", "Radio", "Alert", "DialogActions", "Button", "CircularProgress", "e", "ExportSVGDialog_default"]

package/dist/chunks/{FeatureDialog-XHNPLPWX.js → FeatureDialog-Z5SUYFEB.js}

@@ -1,2 +1,2 @@
 import{a as b}from"./chunk-YOLY6H5C.js";import{a as c}from"./chunk-PFO3G4CM.js";import{H as k,I as F,J as n,K as w,L as E,N as x,g as f,h as T,n as C}from"./chunk-EXFKF6XR.js";import{p as h,r as e}from"./chunk-TEYYBCMF.js";import"./chunk-KVMUXFPB.js";function D(l,a){return[l.accession,l.name,l.description].some(o=>o?.toLowerCase().includes(a))}var z=c(function({model:l,accessions:a}){let o=s=>{for(let m of a)l.setFilter(m,s)};return e.createElement("div",null,e.createElement(f,{onClick:()=>{o(!0)}},"Toggle all on"),e.createElement(f,{onClick:()=>{o(!1)}},"Toggle all off"))}),B=c(function({model:l}){let{annotationTypes:a,annotations:o,featureColors:s,fillPalette:m}=l,[g,v]=h(""),d=g.trim().toLowerCase(),p=[...a.values()].filter(t=>!d||D(t,d)),u=new Map,i=new Map;for(let t of o){let{accession:r}=t;u.set(r,(u.get(r)??0)+1),i.has(r)||i.set(r,s.get(t)?.fill??m[r])}return e.createElement(e.Fragment,null,e.createElement(x,{label:"Filter",size:"small",value:g,onChange:t=>{v(t.target.value)}}),e.createElement(z,{model:l,accessions:p.map(t=>t.accession)}),e.createElement(k,{size:"small"},e.createElement(w,null,e.createElement(E,null,e.createElement(n,{padding:"checkbox"}),e.createElement(n,null,"color"),e.createElement(n,null,"accession"),e.createElement(n,null,"name"),e.createElement(n,null,"count"),e.createElement(n,null,"description"))),e.createElement(F,null,p.map(({accession:t,name:r,description:y})=>e.createElement(E,{key:t},e.createElement(n,{padding:"checkbox"},e.createElement(T,{checked:!l.featureOff(t),onChange:()=>{l.setFilter(t,l.featureOff(t))}})),e.createElement(n,null,e.createElement("div",{style:{width:20,height:20,background:i.get(t)}})),e.createElement(n,null,t),e.createElement(n,null,r),e.createElement(n,null,u.get(t)),e.createElement(n,null,y))))))}),L=c(function({onClose:l,model:a}){return e.createElement(b,{onClose:()=>{l()},open:!0,title:"Feature filters",maxWidth:"xl"},e.createElement(C,null,e.createElement(B,{model:a})))}),A=L;export{A as default};
-//# sourceMappingURL=FeatureDialog-XHNPLPWX.js.map
+//# sourceMappingURL=FeatureDialog-Z5SUYFEB.js.map

package/dist/chunks/{FeatureDialog-XHNPLPWX.js.map → FeatureDialog-Z5SUYFEB.js.map}

@@ -1,6 +1,6 @@
 {
   "version": 3,
-  "sources": ["../../node_modules/.pnpm/react-msaview@9.8.0_4d87629ce60f4a70309a0d727f3e914b/node_modules/react-msaview/src/components/dialogs/FeatureDialog.tsx"],
+  "sources": ["../../node_modules/.pnpm/react-msaview@10.0.0_4d87629ce60f4a70309a0d727f3e914b/node_modules/react-msaview/src/components/dialogs/FeatureDialog.tsx"],
   "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.featureOff(accession)}\n                  onChange={() => {\n                    model.setFilter(accession, model.featureOff(accession))\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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package/dist/chunks/{GapThresholdDialog-MNNNXRMM.js → GapThresholdDialog-B5NC7QTB.js}

@@ -1,2 +1,2 @@
 import{a as p}from"./chunk-YOLY6H5C.js";import{a}from"./chunk-PFO3G4CM.js";import{F as u,S as r,g as m,m as c,n as d}from"./chunk-EXFKF6XR.js";import{p as s,r as e}from"./chunk-TEYYBCMF.js";import"./chunk-KVMUXFPB.js";var f=a(function({model:t}){let[h,l]=s(),i=h??t.allowedGappyness;return e.createElement("div",{style:{display:"flex",alignItems:"center",gap:8}},e.createElement(r,{style:{whiteSpace:"nowrap"}},"\u2265",i,"% gaps"),e.createElement(u,{"data-testid":"gappyness_slider",style:{width:200,marginInline:10},min:1,max:100,value:i,onChange:(y,n)=>{l(n)},onChangeCommitted:(y,n)=>{t.setAllowedGappyness(n),l(void 0)}}))}),g=f;var E=a(function({model:o,onClose:t}){return e.createElement(p,{open:!0,onClose:t,title:"Hide gappy columns"},e.createElement(d,null,e.createElement(r,{variant:"body2",sx:{mb:2}},"The viewer hides each column where at least this share of the rows has a gap."),e.createElement(g,{model:o})),e.createElement(c,null,e.createElement(m,{variant:"contained",onClick:t},"Close")))}),_=E;export{_ as default};
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+//# sourceMappingURL=GapThresholdDialog-B5NC7QTB.js.map

package/dist/chunks/{GapThresholdDialog-MNNNXRMM.js.map → GapThresholdDialog-B5NC7QTB.js.map}

@@ -1,6 +1,6 @@
 {
   "version": 3,
-  "sources": ["../../node_modules/.pnpm/react-msaview@9.8.0_4d87629ce60f4a70309a0d727f3e914b/node_modules/react-msaview/src/components/dialogs/GappynessSlider.tsx", "../../node_modules/.pnpm/react-msaview@9.8.0_4d87629ce60f4a70309a0d727f3e914b/node_modules/react-msaview/src/components/dialogs/GapThresholdDialog.tsx"],
+  "sources": ["../../node_modules/.pnpm/react-msaview@10.0.0_4d87629ce60f4a70309a0d727f3e914b/node_modules/react-msaview/src/components/dialogs/GappynessSlider.tsx", "../../node_modules/.pnpm/react-msaview@10.0.0_4d87629ce60f4a70309a0d727f3e914b/node_modules/react-msaview/src/components/dialogs/GapThresholdDialog.tsx"],
   "sourcesContent": ["import React, { useState } from 'react'\n\nimport { Slider, Typography } from '@mui/material'\nimport { observer } from 'mobx-react'\n\nimport type { MsaViewModel } from '../../model.ts'\n\nconst GappynessSlider = observer(function GappynessSlider({\n  model,\n}: {\n  model: MsaViewModel\n}) {\n  const [dragValue, setDragValue] = useState<number>()\n  const value = dragValue ?? model.allowedGappyness\n  return (\n    <div style={{ display: 'flex', alignItems: 'center', gap: 8 }}>\n      {/* the threshold is inclusive: blanks are columns whose gap count is at\n          least ceil(allowedGappyness% of the rows), so at 100 it hides the\n          columns that are entirely gaps rather than nothing */}\n      <Typography style={{ whiteSpace: 'nowrap' }}>\n        &ge;{value}% gaps\n      </Typography>\n      <Slider\n        // In JBrowse other MUI Sliders share the page, so `.MuiSlider-thumb`\n        // can match the wrong one. Tests and screenshot specs target\n        // `[data-testid=\"gappyness_slider\"] input`, the hidden range input that\n        // takes focus and arrow/PageUp/PageDown.\n        //\n        // Not `slotProps={{ input: ... }}`: that widens `onChange`'s `val` to\n        // `number | number[]`, which setAllowedGappyness rejects.\n        //\n        // The thumb follows local state while dragging and the model takes the\n        // value on release, since each write recomputes the gap columns over\n        // the whole alignment.\n        data-testid=\"gappyness_slider\"\n        style={{ width: 200, marginInline: 10 }}\n        min={1}\n        max={100}\n        value={value}\n        onChange={(_, val) => {\n          setDragValue(val)\n        }}\n        onChangeCommitted={(_, val) => {\n          model.setAllowedGappyness(val)\n          setDragValue(undefined)\n        }}\n      />\n    </div>\n  )\n})\n\nexport default GappynessSlider\n", "import React from 'react'\n\nimport { Dialog } from '@jbrowse/core/ui'\nimport { Button, DialogActions, DialogContent, Typography } from '@mui/material'\nimport { observer } from 'mobx-react'\n\nimport GappynessSlider from './GappynessSlider.tsx'\n\nimport type { MsaViewModel } from '../../model.ts'\n\nconst GapThresholdDialog = observer(function ({\n  model,\n  onClose,\n}: {\n  model: MsaViewModel\n  onClose: () => void\n}) {\n  return (\n    <Dialog open onClose={onClose} title=\"Hide gappy columns\">\n      <DialogContent>\n        <Typography variant=\"body2\" sx={{ mb: 2 }}>\n          The viewer hides each column where at least this share of the rows has\n          a gap.\n        </Typography>\n        <GappynessSlider model={model} />\n      </DialogContent>\n      <DialogActions>\n        <Button variant=\"contained\" onClick={onClose}>\n          Close\n        </Button>\n      </DialogActions>\n    </Dialog>\n  )\n})\n\nexport default GapThresholdDialog\n"],
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package/dist/chunks/{GoToDialog-U3TQYXIE.js → GoToDialog-WWXYDZPR.js}

@@ -1,2 +1,2 @@
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+//# sourceMappingURL=GoToDialog-WWXYDZPR.js.map