jbrowse-plugin-msaview 5.1.1 → 5.3.0

package/dist/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.js

@@ -92,8 +92,6 @@ const PreLoadedMSA = observer(function ({ model, feature, handleClose, preferred
                         feature: selectedTranscript,
                         placement,
                         displayName: getGeneDisplayName(selectedTranscript),
-                        treeAreaWidth: 200,
-                        treeWidth: 100,
                         drawNodeBubbles: false,
                         labelsAlignRight: true,
                         showBranchLen: false,

package/dist/MsaViewPanel/model.d.ts

@@ -111,11 +111,11 @@ 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" | "autoTreeAreaWidth" | "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "treeAreaWidth" | "treeOrder" | "treeWidth" | "bgColor" | "colorSchemeName" | "customColorScheme" | "msaFormat" | "showColumnStats" | "allowedGappyness" | "clades" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "drawMsaLetters" | "encodings" | "features" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "msaFilehandle" | "region" | "relativeTo" | "residueMappings" | "rotated" | "rowHeight" | "rowPanels" | "scrollX" | "scrollY" | "scrollZoom" | "scrollZoomAxis" | "selection" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "trackHeights" | "treeFilehandle" | "treeMetadataFilehandle" | "treeRoot" | "turnedOffFeatures" | "turnedOffTracks"> & Omit<Omit<Omit<{}, "autoTreeAreaWidth" | "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" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "drawMsaLetters" | "encodings" | "features" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "msaFilehandle" | "region" | "relativeTo" | "residueMappings" | "rotated" | "rowHeight" | "rowPanels" | "scrollX" | "scrollY" | "scrollZoom" | "scrollZoomAxis" | "selection" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "trackHeights" | "treeFilehandle" | "treeMetadataFilehandle" | "treeRoot" | "turnedOffFeatures" | "turnedOffTracks"> & Omit<Omit<Omit<{}, "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "treeAreaWidth" | "treeOrder" | "treeWidth"> & {
     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").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
-    treeWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+    treeAreaWidth: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
+    treeWidth: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
     showBranchLen: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     treeOrder: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<import("react-msaview").TreeOrder>, [undefined]>;
     drawTree: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
@@ -123,13 +123,12 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     drawNodeLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     showTreeOverview: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     overviewHeight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
-    autoTreeAreaWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
 }, "bgColor" | "colorSchemeName" | "customColorScheme" | "msaFormat" | "showColumnStats"> & {
     bgColor: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     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("msa-parsers").MSAFormat>>;
+    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" | "drawMsaLetters" | "encodings" | "features" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "msaFilehandle" | "region" | "relativeTo" | "residueMappings" | "rotated" | "rowHeight" | "rowPanels" | "scrollX" | "scrollY" | "scrollZoom" | "scrollZoomAxis" | "selection" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "trackHeights" | "treeFilehandle" | "treeMetadataFilehandle" | "treeRoot" | "turnedOffFeatures" | "turnedOffTracks"> & {
     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]>;
@@ -535,27 +534,26 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     removeActiveDialog(): void;
     queueDialog(cb: (doneCallback: () => void) => [import("@jbrowse/core/util").DialogComponentType, unknown]): void;
 } & {
-    setTreeAreaWidth(n: number): void;
-    setTreeWidth(n: number): void;
+    setTreeAreaWidth(n: number | undefined): void;
+    setTreeWidth(n: number | undefined): void;
     setLabelsAlignRight(arg: boolean): void;
     setDrawTree(arg: boolean): void;
-    setAutoTreeAreaWidth(arg: boolean): void;
     setShowBranchLen(arg: boolean): void;
     setTreeOrder(order: import("react-msaview").TreeOrder): void;
     setDrawNodeBubbles(arg: boolean): void;
     setDrawNodeLabels(arg: boolean): void;
     setShowTreeOverview(arg: boolean): void;
-    setOverviewHeight(n: number): void;
     setDrawLabels(arg: boolean): void;
 } & {
     setColorSchemeName(name: string): void;
     setCustomColorScheme(map?: Record<string, string>): void;
     setBgColor(arg: boolean): void;
     setShowColumnStats(arg: boolean): void;
-    setMSAFormat(arg?: import("msa-parsers").MSAFormat): void;
+    setMSAFormat(arg?: import("react-msaview").MSAFormat): void;
 } & {
     headerHeight: number;
     hideHeader: boolean;
+    importForm: boolean;
     status: {
         msg: string;
         onCancel?: () => void;
@@ -583,7 +581,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     dismissedWarnings: string[];
     resetCount: number;
     hostCarriesData: boolean;
-    annotations: import("msa-parsers").Annotation[];
+    annotations: import("react-msaview").Annotation[];
 } & {
     drawRelativeTo(id: string | undefined): void;
     setHideGaps(arg: boolean): void;
@@ -634,8 +632,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     setGFF(result?: string): void;
 } & {
     readonly hideGapsEffective: boolean;
-    readonly realAllowedGappyness: number;
-    readonly allAnnotations: import("msa-parsers").Annotation[];
+    readonly allAnnotations: import("react-msaview").Annotation[];
     readonly actuallyShowDomains: boolean;
     readonly hostRestoresData: boolean;
     readonly viewInitialized: boolean;
@@ -663,7 +660,7 @@ 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("msa-parsers").MSAParserType | null;
+    readonly MSA: import("react-msaview").MSAParserType | null;
     readonly numColumns: number;
     readonly inputTree: import("react-msaview").NodeWithIds;
     readonly tree: import("react-msaview").NodeWithIds;
@@ -671,6 +668,17 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     readonly rowNamesSet: Map<string, number>;
     readonly resolvedClades: import("react-msaview").ResolvedClade[];
     readonly cladeGutterWidth: number;
+    readonly treeDrawn: boolean;
+    readonly treeTips: {
+        names: string[];
+        depth: number;
+    };
+    readonly maxTipLabelWidth: number;
+    readonly labelColumnWidth: number;
+    readonly fittedTreeAreaWidth: number;
+    readonly effectiveTreeAreaWidth: number;
+    readonly effectiveTreeWidth: number;
+    readonly showTreeText: boolean;
     readonly mouseOverRowName: string | undefined;
     readonly hoveredInsertion: {
         rowName: string;
@@ -681,7 +689,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     readonly treeNewick: string;
     readonly treeOverviewHeight: number;
     readonly treeOverviewLayout: {
-        root: import("react-msaview").HierarchyNode<import("react-msaview").NodeWithIds>;
+        root: import("react-msaview").LaidOutNode<import("react-msaview").NodeWithIds>;
         numTips: number;
         maxDepthToLeaf: number;
         showBranchLen: boolean;
@@ -704,6 +712,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     readonly rows: [string, string][];
     readonly numRows: number;
     seqPosIndex(rowName: string): Int32Array | undefined;
+    rowSequence(name: string): string | undefined;
     readonly rowMap: Map<string, string>;
     readonly columns: Map<string, string>;
     readonly columns2d: string[];
@@ -727,7 +736,6 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     readonly totalHeight: number;
     readonly leaves: import("react-msaview").HierarchyNode<import("react-msaview").NodeWithIds>[];
     readonly rootToTipLength: number;
-    readonly maxBranchLength: number;
     readonly pxPerBranchLength: number;
     readonly maxDepthToLeaf: number;
     readonly allBranchesLength0: boolean;
@@ -736,7 +744,6 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     readonly totalWidth: number;
 } & {
     readonly showMsaLetters: boolean;
-    readonly showTreeText: boolean;
 } & {
     readonly columnTrackContent: Map<string, {
         values?: number[];
@@ -747,9 +754,6 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     columnTrackModel(track: import("react-msaview").ColumnTrackSpec): import("react-msaview").BasicTrack;
     readonly columnTrackModels: import("react-msaview").BasicTrack[];
 } & {
-    readonly labelWidthMap: Map<string, number>;
-    readonly labelWidthScale: number;
-    readonly labelsWidth: number;
     readonly secondaryStructureConsensus: string | undefined;
     readonly secondaryStructureArcs: import("react-msaview").Arc[] | undefined;
     readonly adapterTrackModels: import("react-msaview").BasicTrack[];
@@ -787,9 +791,9 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     readonly topBandHeight: number;
     readonly msaAreaHeight: number;
     readonly totalTrackAreaHeight: number;
-    readonly annotationTypes: Map<string, import("msa-parsers").Annotation>;
-    readonly filteredAnnotations: import("msa-parsers").Annotation[];
-    readonly annotationsByRow: Record<string, import("msa-parsers").Annotation[]>;
+    readonly annotationTypes: Map<string, import("react-msaview").Annotation>;
+    readonly filteredAnnotations: import("react-msaview").Annotation[];
+    readonly annotationsByRow: Record<string, import("react-msaview").Annotation[]>;
 } & {
     readonly showVerticalScrollbar: boolean;
 } & {
@@ -817,17 +821,12 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     replaceTree(newick: string): void;
     resetZoom(): void;
     zoomAtCenter(scaleFactor: number, axis?: "both" | "horizontal" | "vertical"): void;
-    zoomOutHorizontal(): void;
-    zoomInHorizontal(): void;
-    zoomInVertical(): void;
-    zoomOutVertical(): void;
     zoomIn(): void;
     zoomOut(): void;
     zoomToPos(scaleFactor: number, offsetX: number, offsetY: number, axis?: "both" | "horizontal" | "vertical"): void;
     doScrollY(deltaY: number): void;
     setScrollY(n: number): void;
-    setAnnotations(annotations: import("msa-parsers").Annotation[]): void;
-    setDomains(data?: Record<string, import("msa-parsers").InterProScanResults>): void;
+    setAnnotations(annotations: import("react-msaview").Annotation[]): void;
     applyGFFText(gffText: string): void;
     doScrollX(deltaX: number): void;
     setScrollX(n: number): void;
@@ -846,24 +845,24 @@ 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("msa-parsers").Annotation[];
-    readonly categoricalDomainTypes: import("msa-parsers").Annotation[];
+    readonly segmentDomainTypes: import("react-msaview").Annotation[];
+    readonly categoricalDomainTypes: import("react-msaview").Annotation[];
     readonly fillPalette: {
         [x: string]: string;
     };
     readonly featureFillEncoding: import("react-msaview").ResolvedEncoding | undefined;
-    readonly featureColors: Map<import("msa-parsers").Annotation, {
+    readonly featureColors: Map<import("react-msaview").Annotation, {
         fill: string;
         stroke: string;
     }>;
-    readonly featureLabels: Map<import("msa-parsers").Annotation, string> | undefined;
+    readonly featureLabels: Map<import("react-msaview").Annotation, string> | undefined;
     readonly segmentLabels: Map<string, string>;
-    readonly visibleDomainTypes: import("msa-parsers").Annotation[];
+    readonly visibleDomainTypes: import("react-msaview").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("msa-parsers").Annotation[];
+    readonly mouseOverDomains: import("react-msaview").Annotation[];
     readonly referenceRowIndex: number | undefined;
     readonly hoveredRowIndices: number[];
     readonly highlightedColumnRuns: {
@@ -904,13 +903,13 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
         x: "column" | "position";
         kind: "features";
         field?: string | undefined;
-        colors: Map<import("msa-parsers").Annotation, {
+        colors: Map<import("react-msaview").Annotation, {
             fill: string;
             stroke: string;
         }>;
         legend: import("react-msaview").LegendEntry[];
         legendTitle?: string | undefined;
-        labels?: Map<import("msa-parsers").Annotation, string> | undefined;
+        labels?: Map<import("react-msaview").Annotation, string> | undefined;
     })[];
     readonly resolvedRowPanels: import("react-msaview").ResolvedRowPanel[];
     readonly featureAlignShifts: Map<string, Map<string, number>>;
@@ -920,6 +919,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
 } & {
     setHeaderHeight(arg: number): void;
     setHideHeader(arg: boolean): void;
+    setImportForm(arg: boolean): void;
     treeOverviewClick(y: number): void;
     setTrackHeight(heightKey: string, height: number): void;
     reset(): void;
@@ -929,6 +929,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     fit(): void;
     fitVertically(): void;
     zoomToRegion(region: import("react-msaview").Region): void;
+    revealRegion(region: import("react-msaview").Region): void;
     zoomToSelection(): void;
     selectBlock(anchor: {
         col: number;
@@ -1122,11 +1123,11 @@ 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" | "autoTreeAreaWidth" | "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "treeAreaWidth" | "treeOrder" | "treeWidth" | "bgColor" | "colorSchemeName" | "customColorScheme" | "msaFormat" | "showColumnStats" | "allowedGappyness" | "clades" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "drawMsaLetters" | "encodings" | "features" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "msaFilehandle" | "region" | "relativeTo" | "residueMappings" | "rotated" | "rowHeight" | "rowPanels" | "scrollX" | "scrollY" | "scrollZoom" | "scrollZoomAxis" | "selection" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "trackHeights" | "treeFilehandle" | "treeMetadataFilehandle" | "treeRoot" | "turnedOffFeatures" | "turnedOffTracks"> & Omit<Omit<Omit<{}, "autoTreeAreaWidth" | "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" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "drawMsaLetters" | "encodings" | "features" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "msaFilehandle" | "region" | "relativeTo" | "residueMappings" | "rotated" | "rowHeight" | "rowPanels" | "scrollX" | "scrollY" | "scrollZoom" | "scrollZoomAxis" | "selection" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "trackHeights" | "treeFilehandle" | "treeMetadataFilehandle" | "treeRoot" | "turnedOffFeatures" | "turnedOffTracks"> & Omit<Omit<Omit<{}, "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "treeAreaWidth" | "treeOrder" | "treeWidth"> & {
     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").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
-    treeWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+    treeAreaWidth: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
+    treeWidth: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
     showBranchLen: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     treeOrder: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<import("react-msaview").TreeOrder>, [undefined]>;
     drawTree: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
@@ -1134,13 +1135,12 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     drawNodeLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     showTreeOverview: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     overviewHeight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
-    autoTreeAreaWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
 }, "bgColor" | "colorSchemeName" | "customColorScheme" | "msaFormat" | "showColumnStats"> & {
     bgColor: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     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("msa-parsers").MSAFormat>>;
+    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" | "drawMsaLetters" | "encodings" | "features" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "msaFilehandle" | "region" | "relativeTo" | "residueMappings" | "rotated" | "rowHeight" | "rowPanels" | "scrollX" | "scrollY" | "scrollZoom" | "scrollZoomAxis" | "selection" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "trackHeights" | "treeFilehandle" | "treeMetadataFilehandle" | "treeRoot" | "turnedOffFeatures" | "turnedOffTracks"> & {
     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]>;
@@ -1523,16 +1523,16 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     dataStoreId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     launchCompleted: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     mafRegion: import("@jbrowse/mobx-state-tree").IType<MafRegion | undefined, MafRegion | undefined, MafRegion | undefined>;
-}>, "id" | "type" | "autoTreeAreaWidth" | "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "treeAreaWidth" | "treeOrder" | "treeWidth" | "bgColor" | "colorSchemeName" | "customColorScheme" | "msaFormat" | "showColumnStats" | "allowedGappyness" | "clades" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "drawMsaLetters" | "encodings" | "features" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "msaFilehandle" | "region" | "relativeTo" | "residueMappings" | "rotated" | "rowHeight" | "rowPanels" | "scrollX" | "scrollY" | "scrollZoom" | "scrollZoomAxis" | "selection" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "trackHeights" | "treeFilehandle" | "treeMetadataFilehandle" | "treeRoot" | "turnedOffFeatures" | "turnedOffTracks"> & ({
+}>, "id" | "type" | "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "treeAreaWidth" | "treeOrder" | "treeWidth" | "bgColor" | "colorSchemeName" | "customColorScheme" | "msaFormat" | "showColumnStats" | "allowedGappyness" | "clades" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "drawMsaLetters" | "encodings" | "features" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "msaFilehandle" | "region" | "relativeTo" | "residueMappings" | "rotated" | "rowHeight" | "rowPanels" | "scrollX" | "scrollY" | "scrollZoom" | "scrollZoomAxis" | "selection" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "trackHeights" | "treeFilehandle" | "treeMetadataFilehandle" | "treeRoot" | "turnedOffFeatures" | "turnedOffTracks"> & ({
     bgColor: boolean;
     colorSchemeName: string;
     customColorScheme: Record<string, string> | undefined;
     showColumnStats: boolean;
-    msaFormat: import("msa-parsers").MSAFormat | undefined;
+    msaFormat: import("react-msaview").MSAFormat | undefined;
     drawLabels: boolean;
     labelsAlignRight: boolean;
-    treeAreaWidth: number;
-    treeWidth: number;
+    treeAreaWidth: number | undefined;
+    treeWidth: number | undefined;
     showBranchLen: boolean;
     treeOrder: import("react-msaview").TreeOrder;
     drawTree: boolean;
@@ -1540,7 +1540,6 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     drawNodeLabels: boolean;
     showTreeOverview: boolean;
     overviewHeight: number;
-    autoTreeAreaWidth: boolean;
     columnTracks: import("react-msaview").ColumnTrackSpec[];
     id: string;
     showDomains: boolean;
@@ -1666,11 +1665,11 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     colorSchemeName: string;
     customColorScheme: Record<string, string> | undefined;
     showColumnStats: boolean;
-    msaFormat: import("msa-parsers").MSAFormat | undefined;
+    msaFormat: import("react-msaview").MSAFormat | undefined;
     drawLabels: boolean;
     labelsAlignRight: boolean;
-    treeAreaWidth: number;
-    treeWidth: number;
+    treeAreaWidth: number | undefined;
+    treeWidth: number | undefined;
     showBranchLen: boolean;
     treeOrder: import("react-msaview").TreeOrder;
     drawTree: boolean;
@@ -1678,7 +1677,6 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     drawNodeLabels: boolean;
     showTreeOverview: boolean;
     overviewHeight: number;
-    autoTreeAreaWidth: boolean;
     columnTracks?: undefined;
     id: string;
     showDomains: boolean;

package/dist/chunks/AboutDialog-447TIFAW.js

@@ -0,0 +1,2 @@
+import{a as l}from"./chunk-6EOYBBT4.js";import{a as i}from"./chunk-DNFD5II2.js";import{a as m}from"./chunk-BX4Z274Q.js";import{a}from"./chunk-J6KYLXRD.js";import{b as r}from"./chunk-FY3BTKY4.js";var e=r(a(),1),o=r(i(),1),t=r(m(),1);function c({onClose:n}){return e.default.createElement(o.Dialog,{open:!0,title:"About",onClose:()=>{n()}},e.default.createElement(t.DialogContent,null,e.default.createElement(t.Typography,null,"MSAView ",l," (",e.default.createElement(t.Link,{target:"_blank",rel:"noopener",href:"https://github.com/gmod/react-msaview"},"Github"),")"),e.default.createElement("ul",null,e.default.createElement("li",null,e.default.createElement(t.Typography,null,"We use some color schemes from the"," ",e.default.createElement(t.Link,{target:"_blank",rel:"noopener",href:"https://github.com/biotite-dev/biotite"},"biotite")," ","project, and their license is reproduced"," ",e.default.createElement(t.Link,{target:"_blank",rel:"noopener",href:"https://github.com/biotite-dev/biotite/blob/master/LICENSE.rst"},"here"))),e.default.createElement("li",null,e.default.createElement(t.Typography,null,"See this page for some information on jalview colorings"," ",e.default.createElement(t.Link,{target:"_blank",rel:"noopener",href:"https://www.jalview.org/help/html/colourSchemes/"},"here"))),e.default.createElement("li",null,e.default.createElement(t.Typography,null,"See this page for some info on the clustal, cinema, maeditor, and lesk color schemes"," ",e.default.createElement(t.Link,{target:"_blank",rel:"noopener",href:"http://www.bioinformatics.nl/~berndb/aacolour.html"},"here"))),e.default.createElement("li",null,e.default.createElement(t.Typography,null,"See this paper about the flower color scheme"," ",e.default.createElement(t.Link,{target:"_blank",rel:"noopener",href:"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7245768/"},"here"))))))}export{c as default};
+//# sourceMappingURL=AboutDialog-447TIFAW.js.map

package/dist/chunks/{AboutDialog-YNPKL64P.js.map → AboutDialog-447TIFAW.js.map}

@@ -1,7 +1,7 @@
 {
   "version": 3,
-  "sources": ["../../node_modules/.pnpm/react-msaview@8.4.1_3e54acfe76b6ad0d26e91cd532b7f775/node_modules/react-msaview/src/components/dialogs/AboutDialog.tsx", "../../node_modules/.pnpm/react-msaview@8.4.1_3e54acfe76b6ad0d26e91cd532b7f775/node_modules/react-msaview/src/version.ts"],
-  "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", "export const version = '8.4.1'\n"],
-  "mappings": "2JAAA,IAAAA,EAAkB,SAElBC,EAAuB,SACvBC,EAAgD,SCHzC,IAAMC,EAAU,QDOT,SAAPC,EAA6B,CAAE,QAAAC,CAAO,EAA2B,CACtE,OACE,EAAAC,QAAA,cAAC,SAAM,CACL,KAAI,GACJ,MAAM,QACN,QAAS,IAAK,CACZD,EAAO,CACT,CAAC,EAED,EAAAC,QAAA,cAAC,gBAAa,KACZ,EAAAA,QAAA,cAAC,aAAU,gBACAC,OACT,EAAAD,QAAA,cAAC,OAAI,CACH,OAAO,SACP,IAAI,WACJ,KAAK,uCAAuC,EAAA,QAAA,OAOhD,EAAAA,QAAA,cAAA,KAAA,KACE,EAAAA,QAAA,cAAA,KAAA,KACE,EAAAA,QAAA,cAAC,aAAU,0CAC0B,IACnC,EAAAA,QAAA,cAAC,OAAI,CACH,OAAO,SACP,IAAI,WACJ,KAAK,wCAAwC,EAAA,SAAA,EAGvC,+CACiC,IACzC,EAAAA,QAAA,cAAC,OAAI,CACH,OAAO,SACP,IAAI,WACJ,KAAK,gEAAgE,EAAA,MAAA,CAGhE,CACI,EAEf,EAAAA,QAAA,cAAA,KAAA,KACE,EAAAA,QAAA,cAAC,aAAU,+DAC+C,IACxD,EAAAA,QAAA,cAAC,OAAI,CACH,OAAO,SACP,IAAI,WACJ,KAAK,kDAAkD,EAAA,MAAA,CAGlD,CACI,EAEf,EAAAA,QAAA,cAAA,KAAA,KACE,EAAAA,QAAA,cAAC,aAAU,4FAEU,IACnB,EAAAA,QAAA,cAAC,OAAI,CACH,OAAO,SACP,IAAI,WACJ,KAAK,oDAAoD,EAAA,MAAA,CAGpD,CACI,EAEf,EAAAA,QAAA,cAAA,KAAA,KACE,EAAAA,QAAA,cAAC,aAAU,oDACoC,IAC7C,EAAAA,QAAA,cAAC,OAAI,CACH,OAAO,SACP,IAAI,WACJ,KAAK,uDAAuD,EAAA,MAAA,CAGvD,CACI,CACV,CACF,CACS,CAGtB",
-  "names": ["import_react", "import_ui", "import_material", "version", "AboutDialog", "onClose", "React", "version"]
+  "sources": ["../../node_modules/.pnpm/react-msaview@9.1.0_3e54acfe76b6ad0d26e91cd532b7f775/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": "mMAAA,IAAAA,EAAkB,SAElBC,EAAuB,SACvBC,EAAgD,SAIlC,SAAPC,EAA6B,CAAE,QAAAC,CAAO,EAA2B,CACtE,OACE,EAAAC,QAAA,cAAC,SAAM,CACL,KAAI,GACJ,MAAM,QACN,QAAS,IAAK,CACZD,EAAO,CACT,CAAC,EAED,EAAAC,QAAA,cAAC,gBAAa,KACZ,EAAAA,QAAA,cAAC,aAAU,gBACAC,OACT,EAAAD,QAAA,cAAC,OAAI,CACH,OAAO,SACP,IAAI,WACJ,KAAK,uCAAuC,EAAA,QAAA,OAOhD,EAAAA,QAAA,cAAA,KAAA,KACE,EAAAA,QAAA,cAAA,KAAA,KACE,EAAAA,QAAA,cAAC,aAAU,0CAC0B,IACnC,EAAAA,QAAA,cAAC,OAAI,CACH,OAAO,SACP,IAAI,WACJ,KAAK,wCAAwC,EAAA,SAAA,EAGvC,+CACiC,IACzC,EAAAA,QAAA,cAAC,OAAI,CACH,OAAO,SACP,IAAI,WACJ,KAAK,gEAAgE,EAAA,MAAA,CAGhE,CACI,EAEf,EAAAA,QAAA,cAAA,KAAA,KACE,EAAAA,QAAA,cAAC,aAAU,+DAC+C,IACxD,EAAAA,QAAA,cAAC,OAAI,CACH,OAAO,SACP,IAAI,WACJ,KAAK,kDAAkD,EAAA,MAAA,CAGlD,CACI,EAEf,EAAAA,QAAA,cAAA,KAAA,KACE,EAAAA,QAAA,cAAC,aAAU,4FAEU,IACnB,EAAAA,QAAA,cAAC,OAAI,CACH,OAAO,SACP,IAAI,WACJ,KAAK,oDAAoD,EAAA,MAAA,CAGpD,CACI,EAEf,EAAAA,QAAA,cAAA,KAAA,KACE,EAAAA,QAAA,cAAC,aAAU,oDACoC,IAC7C,EAAAA,QAAA,cAAC,OAAI,CACH,OAAO,SACP,IAAI,WACJ,KAAK,uDAAuD,EAAA,MAAA,CAGvD,CACI,CACV,CACF,CACS,CAGtB",
+  "names": ["import_react", "import_ui", "import_material", "AboutDialog", "onClose", "React", "version"]
 }

package/dist/chunks/AnnotationFileDialog-S3N5EHHE.js

@@ -0,0 +1,2 @@
+import{g as E}from"./chunk-DEFUNIWW.js";import"./chunk-K55ZVN73.js";import"./chunk-73KAPCJ2.js";import{a as x}from"./chunk-CVLB4VFP.js";import{a as C}from"./chunk-DNFD5II2.js";import{a as w}from"./chunk-BX4Z274Q.js";import{a as y}from"./chunk-J6KYLXRD.js";import{b as i}from"./chunk-FY3BTKY4.js";var e=i(y(),1),c=i(C(),1),t=i(w(),1),d=i(x(),1);async function T(o){let l=await fetch(o);if(!l.ok)throw new Error(`HTTP ${l.status} fetching ${o} ${await l.text()}`);return l.text()}var b=(0,d.observer)(function({handleClose:o,model:l}){let[a,h]=(0,e.useState)(),[r,g]=(0,e.useState)("file"),[s,F]=(0,e.useState)(""),[m,u]=(0,e.useState)(),[v,f]=(0,e.useState)(!1);return e.default.createElement(c.Dialog,{maxWidth:"xl",title:"Open annotation file",onClose:()=>{o()},open:!0},e.default.createElement(t.DialogContent,null,m?e.default.createElement(c.ErrorMessage,{error:m}):null,e.default.createElement(t.Typography,null,"Open a GFF3 file of annotations, such as the one `react-msaview-cli interpro` writes, or the JSON an InterProScan run returns."),e.default.createElement("div",{style:{display:"flex",margin:30}},e.default.createElement(t.FormControl,{component:"fieldset"},e.default.createElement(t.RadioGroup,{value:r,onChange:n=>{g(n.target.value)}},e.default.createElement(t.FormControlLabel,{value:"url",control:e.default.createElement(t.Radio,null),label:"URL"}),e.default.createElement(t.FormControlLabel,{value:"file",control:e.default.createElement(t.Radio,null),label:"File"}))),r==="url"?e.default.createElement("div",null,e.default.createElement(t.Typography,null,"Open an annotation file from a URL"),e.default.createElement(t.TextField,{label:"URL",value:s,onChange:n=>{F(n.target.value)}})):e.default.createElement("div",{style:{paddingTop:20}},e.default.createElement(t.Typography,null,"Open an annotation file from your local drive"),e.default.createElement(t.Button,{variant:"outlined",component:"label"},"Choose File",e.default.createElement("input",{type:"file",hidden:!0,onChange:({target:n})=>{let p=n.files?.[0];p&&h(p)}})),a?e.default.createElement(t.Typography,null,a.name):null))),e.default.createElement(t.DialogActions,null,e.default.createElement(t.Button,{variant:"contained",color:"primary",disabled:v||(r==="file"?!a:!s.trim()),onClick:()=>{(async()=>{f(!0),u(void 0);try{let n=await(r==="file"&&a?a.text():T(s));l.setGFFFilehandle(void 0),l.setGFF(E(n)),l.setShowDomains(!0),o()}catch(n){console.error(n),u(n)}finally{f(!1)}})()}},"Open annotations"),e.default.createElement(t.Button,{variant:"contained",color:"secondary",onClick:()=>{o()}},"Cancel")))}),R=b;export{R as default};
+//# sourceMappingURL=AnnotationFileDialog-S3N5EHHE.js.map

package/dist/chunks/AnnotationFileDialog-S3N5EHHE.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../node_modules/.pnpm/react-msaview@9.1.0_3e54acfe76b6ad0d26e91cd532b7f775/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  Radio,\n  RadioGroup,\n  TextField,\n  Typography,\n} from '@mui/material'\nimport { observer } from 'mobx-react'\nimport { annotationTextToGFF } from 'msa-parsers'\n\nimport type { MsaViewModel } from '../../model.ts'\n\nasync function fetchText(url: string) {\n  const response = await fetch(url)\n  if (!response.ok) {\n    throw new Error(\n      `HTTP ${response.status} fetching ${url} ${await response.text()}`,\n    )\n  }\n  return response.text()\n}\n\nconst AnnotationFileDialog = observer(function ({\n  handleClose,\n  model,\n}: {\n  handleClose: () => void\n  model: MsaViewModel\n}) {\n  const [file, setFile] = useState<File>()\n  const [choice, setChoice] = useState('file')\n  const [url, setUrl] = useState('')\n  const [error, setError] = useState<unknown>()\n  const [loading, setLoading] = useState(false)\n\n  // the error is shown here rather than notified: the standalone app and the\n  // MSAViewer component have no jbrowse session to notify, and asking one for\n  // its notify() threw out of the success path into the catch, which threw\n  // again on the same missing session\n  return (\n    <Dialog\n      maxWidth=\"xl\"\n      title=\"Open annotation file\"\n      onClose={() => {\n        handleClose()\n      }}\n      open\n    >\n      <DialogContent>\n        {error ? <ErrorMessage error={error} /> : null}\n        <Typography>\n          Open a GFF3 file of annotations, such as the one `react-msaview-cli\n          interpro` writes, or the JSON an InterProScan run returns.\n        </Typography>\n\n        <div style={{ display: 'flex', margin: 30 }}>\n          <FormControl component=\"fieldset\">\n            <RadioGroup\n              value={choice}\n              onChange={event => {\n                setChoice(event.target.value)\n              }}\n            >\n              <FormControlLabel value=\"url\" control={<Radio />} label=\"URL\" />\n              <FormControlLabel value=\"file\" control={<Radio />} label=\"File\" />\n            </RadioGroup>\n          </FormControl>\n          {choice === 'url' ? (\n            <div>\n              <Typography>Open an annotation file from a URL</Typography>\n              <TextField\n                label=\"URL\"\n                value={url}\n                onChange={event => {\n                  setUrl(event.target.value)\n                }}\n              />\n            </div>\n          ) : (\n            <div style={{ paddingTop: 20 }}>\n              <Typography>\n                Open an annotation file from your local drive\n              </Typography>\n              <Button variant=\"outlined\" component=\"label\">\n                Choose File\n                <input\n                  type=\"file\"\n                  hidden\n                  onChange={({ target }) => {\n                    const chosen = target.files?.[0]\n                    if (chosen) {\n                      setFile(chosen)\n                    }\n                  }}\n                />\n              </Button>\n              {file ? <Typography>{file.name}</Typography> : null}\n            </div>\n          )}\n        </div>\n      </DialogContent>\n      <DialogActions>\n        <Button\n          variant=\"contained\"\n          color=\"primary\"\n          disabled={loading || (choice === 'file' ? !file : !url.trim())}\n          onClick={() => {\n            // eslint-disable-next-line @typescript-eslint/no-floating-promises\n            ;(async () => {\n              setLoading(true)\n              setError(undefined)\n              try {\n                const text = await (choice === 'file' && file\n                  ? file.text()\n                  : fetchText(url))\n                // through the model's own GFF text, so the annotations travel\n                // in the snapshot and the shared URL like every other layer. A\n                // filehandle left set would make the snapshot drop that text\n                model.setGFFFilehandle(undefined)\n                model.setGFF(annotationTextToGFF(text))\n                model.setShowDomains(true)\n                handleClose()\n              } catch (e) {\n                console.error(e)\n                setError(e)\n              } finally {\n                setLoading(false)\n              }\n            })()\n          }}\n        >\n          Open annotations\n        </Button>\n        <Button\n          variant=\"contained\"\n          color=\"secondary\"\n          onClick={() => {\n            handleClose()\n          }}\n        >\n          Cancel\n        </Button>\n      </DialogActions>\n    </Dialog>\n  )\n})\n\nexport default AnnotationFileDialog\n"],
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+  "names": ["import_react", "import_ui", "import_material", "import_mobx_react", "fetchText", "url", "response", "AnnotationFileDialog", "handleClose", "model", "file", "setFile", "choice", "setChoice", "setUrl", "error", "setError", "loading", "setLoading", "React", "event", "target", "chosen", "text", "annotationTextToGFF", "e", "AnnotationFileDialog_default"]
+}

package/dist/chunks/ExportSVGDialog-7ZHKKQ7W.js

@@ -0,0 +1,2 @@
+import{a as p}from"./chunk-ERCMNTEQ.js";import{X as v,Y as y}from"./chunk-OVAXNTPN.js";import{a as L}from"./chunk-CVLB4VFP.js";import{a as D}from"./chunk-DNFD5II2.js";import{a as V}from"./chunk-BX4Z274Q.js";import{a as I}from"./chunk-J6KYLXRD.js";import{b as l}from"./chunk-FY3BTKY4.js";var t=l(I(),1),i=l(D(),1),e=l(V(),1),k=l(L(),1);function z(r){requestAnimationFrame(()=>{requestAnimationFrame(r)})}var P=(0,k.observer)(function({model:r,onClose:c}){let[s,C]=(0,t.useState)(!0),[n,T]=(0,t.useState)(!0),[o,b]=(0,t.useState)("viewport"),[E,w]=(0,t.useState)(),[m,h]=(0,t.useState)(!1),d=(0,e.useTheme)(),{turnedOnTracks:M,numColumns:S,leaves:A,showMsaLetters:F}=r,g=M.length>0,x=y(r,v(r,{theme:d,exportType:"entire",includeTracks:n})),f=F&&o==="entire"?S*A.length:0,G=f>1e5;return t.default.createElement(i.Dialog,{onClose:()=>{c()},open:!0,title:"Export SVG"},t.default.createElement(e.DialogContent,null,E?t.default.createElement(i.ErrorMessage,{error:E}):null,t.default.createElement(e.Typography,null,"Settings:"),t.default.createElement(p,{label:"Include minimap?",disabled:o==="entire",checked:s,onChange:()=>{C(!s)}}),g?t.default.createElement(p,{label:"Include tracks?",checked:n,onChange:()=>{T(!n)}}):null,t.default.createElement("div",null,t.default.createElement(e.FormControl,null,t.default.createElement(e.FormLabel,null,"Export type"),t.default.createElement(e.RadioGroup,{value:o,onChange:a=>{let{value:u}=a.target;(u==="entire"||u==="viewport")&&b(u)}},t.default.createElement(e.FormControlLabel,{value:"entire",control:t.default.createElement(e.Radio,null),label:"Entire MSA"}),t.default.createElement(e.FormControlLabel,{value:"viewport",control:t.default.createElement(e.Radio,null),label:"Current viewport only"})))),G?t.default.createElement(e.Alert,{severity:"warning",style:{marginTop:8}},"The entire MSA is ",Math.round(x.width),"x",Math.round(x.height)," pixels and draws"," ",Math.round(f/1e3),"k residue letters, each its own SVG element. Export may be slow or fail \u2014 zooming out far enough to hide the letters exports the same alignment as an image instead."):null),t.default.createElement(e.DialogActions,null,t.default.createElement(e.Button,{variant:"contained",color:"primary",disabled:m,startIcon:m?t.default.createElement(e.CircularProgress,{size:16,color:"inherit"}):null,onClick:()=>{h(!0),z(()=>{r.exportSVG({theme:d,includeMinimap:s,includeTracks:g&&n,exportType:o}).then(()=>{c()}).catch(a=>{console.error(a),w(a)}).finally(()=>{h(!1)})})}},m?"Exporting\u2026":"Export"),t.default.createElement(e.Button,{variant:"contained",color:"secondary",onClick:()=>{c()}},"Cancel")))}),B=P;export{B as default};
+//# sourceMappingURL=ExportSVGDialog-7ZHKKQ7W.js.map

package/dist/chunks/ExportSVGDialog-7ZHKKQ7W.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../node_modules/.pnpm/react-msaview@9.1.0_3e54acfe76b6ad0d26e91cd532b7f775/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": ["import_react", "import_ui", "import_material", "import_mobx_react", "afterPaint", "fn", "ExportSVGDialog", "model", "onClose", "includeMinimap", "setIncludeMinimap", "includeTracks", "setIncludeTracks", "exportType", "setExportType", "error", "setError", "exporting", "setExporting", "theme", "turnedOnTracks", "numColumns", "leaves", "showMsaLetters", "hasTracks", "entire", "exportPageSize", "getLayout", "glyphs", "isLargeExport", "React", "Checkbox2", "event", "value", "e", "ExportSVGDialog_default"]
+}

package/dist/chunks/{FeatureDialog-7XXL6XUK.js → FeatureDialog-EEOGSLOG.js}

@@ -1,2 +1,2 @@
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-//# sourceMappingURL=FeatureDialog-7XXL6XUK.js.map
+//# sourceMappingURL=FeatureDialog-EEOGSLOG.js.map

package/dist/chunks/{FeatureDialog-7XXL6XUK.js.map → FeatureDialog-EEOGSLOG.js.map}

@@ -1,6 +1,6 @@
 {
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+  "sources": ["../../node_modules/.pnpm/react-msaview@9.1.0_3e54acfe76b6ad0d26e91cd532b7f775/node_modules/react-msaview/src/components/dialogs/FeatureDialog.tsx"],
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   "names": ["import_react", "import_ui", "import_material", "import_mobx_react", "matches", "type", "query", "field", "Toggles", "model", "accessions", "setAll", "shown", "accession", "React", "FeatureTable", "annotationTypes", "annotations", "featureColors", "fillPalette", "setQuery", "needle", "types", "counts", "swatches", "annot", "event", "t", "name", "description", "FeatureTypeDialog", "onClose", "FeatureDialog_default"]

package/dist/chunks/HelpDialog-TCWNBZOV.js

@@ -0,0 +1,2 @@
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+//# sourceMappingURL=HelpDialog-TCWNBZOV.js.map

package/dist/chunks/HelpDialog-TCWNBZOV.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../node_modules/.pnpm/react-msaview@9.1.0_3e54acfe76b6ad0d26e91cd532b7f775/node_modules/react-msaview/src/components/dialogs/HelpDialog.tsx"],
+  "sourcesContent": ["import React, { lazy } from 'react'\n\nimport { Dialog } from '@jbrowse/core/ui'\nimport {\n  Button,\n  DialogActions,\n  DialogContent,\n  Table,\n  TableBody,\n  TableCell,\n  TableRow,\n  Typography,\n} from '@mui/material'\n\nimport { version } from '../../version.ts'\nimport { keyboardControls, mouseControls } from '../controls.ts'\n\nimport type { MsaViewModel } from '../../model.ts'\nimport type { Control } from '../controls.ts'\n\nconst AboutDialog = lazy(() => import('./AboutDialog.tsx'))\n\nfunction ControlTable({ title, rows }: { title: string; rows: Control[] }) {\n  return (\n    <>\n      <Typography variant=\"subtitle2\" sx={{ mt: 1 }}>\n        {title}\n      </Typography>\n      <Table size=\"small\" aria-label={title}>\n        <TableBody>\n          {rows.map(({ label, action }) => (\n            <TableRow key={label}>\n              <TableCell sx={{ whiteSpace: 'nowrap', fontWeight: 500 }}>\n                {label}\n              </TableCell>\n              <TableCell>{action}</TableCell>\n            </TableRow>\n          ))}\n        </TableBody>\n      </Table>\n    </>\n  )\n}\n\nexport default function HelpDialog({\n  model,\n  onClose,\n}: {\n  model: MsaViewModel\n  onClose: () => void\n}) {\n  return (\n    <Dialog open title=\"Mouse & keyboard\" onClose={onClose}>\n      <DialogContent>\n        <ControlTable title=\"Mouse\" rows={mouseControls} />\n        <ControlTable\n          title=\"Keyboard (click the alignment first)\"\n          rows={keyboardControls}\n        />\n      </DialogContent>\n      <DialogActions>\n        <Typography variant=\"caption\" sx={{ mr: 'auto', pl: 1 }}>\n          MSAView {version}\n        </Typography>\n        <Button\n          onClick={() => {\n            model.queueDialog(done => [AboutDialog, { onClose: done }])\n            onClose()\n          }}\n        >\n          About & credits\n        </Button>\n        <Button variant=\"contained\" onClick={onClose}>\n          Close\n        </Button>\n      </DialogActions>\n    </Dialog>\n  )\n}\n"],
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+  "names": ["import_react", "import_ui", "import_material", "AboutDialog", "ControlTable", "title", "rows", "React", "label", "action", "HelpDialog", "model", "onClose", "mouseControls", "keyboardControls", "version", "done"]
+}