jbrowse-plugin-msaview 3.5.0 → 3.7.0

package/dist/MsaViewPanel/model.d.ts

@@ -7,6 +7,7 @@ import type { TranscriptRef } from './util';
 import type { MenuItem } from '@jbrowse/core/ui';
 import type { Instance } from '@jbrowse/mobx-state-tree';
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
+import type { Region } from 'react-msaview';
 type LGV = LinearGenomeViewModel;
 type MaybeLGV = LGV | undefined;
 export interface IRegion {
@@ -110,8 +111,8 @@ export interface OrthologParams {
 export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelType<Omit<Omit<{
     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").IType<boolean | undefined, boolean, boolean>;
-}, "id" | "type" | "autoTreeAreaWidth" | "drawLabels" | "drawNodeBubbles" | "drawTree" | "labelsAlignRight" | "showBranchLen" | "treeAreaWidth" | "treeWidth" | "bgColor" | "colorSchemeName" | "msaFormat" | "showColumnStats" | "allowedGappyness" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "drawMsaLetters" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "msaFilehandle" | "relativeTo" | "residueMappings" | "rowHeight" | "scrollX" | "scrollY" | "scrollZoom" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "treeFilehandle" | "treeMetadataFilehandle" | "turnedOffFeatures" | "turnedOffTracks"> & Omit<Omit<Omit<{}, "autoTreeAreaWidth" | "drawLabels" | "drawNodeBubbles" | "drawTree" | "labelsAlignRight" | "showBranchLen" | "treeAreaWidth" | "treeWidth"> & {
+    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" | "treeWidth" | "bgColor" | "colorSchemeName" | "msaFormat" | "showColumnStats" | "allowedGappyness" | "clades" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "drawMsaLetters" | "encodings" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "msaFilehandle" | "relativeTo" | "residueMappings" | "rowHeight" | "rowPanels" | "scrollX" | "scrollY" | "scrollZoom" | "scrollZoomAxis" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "trackHeights" | "treeFilehandle" | "treeMetadataFilehandle" | "turnedOffFeatures" | "turnedOffTracks"> & Omit<Omit<Omit<{}, "autoTreeAreaWidth" | "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "treeAreaWidth" | "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]>;
@@ -119,22 +120,26 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     showBranchLen: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     drawTree: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     drawNodeBubbles: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    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" | "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]>;
     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" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "drawMsaLetters" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "msaFilehandle" | "relativeTo" | "residueMappings" | "rowHeight" | "scrollX" | "scrollY" | "scrollZoom" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "treeFilehandle" | "treeMetadataFilehandle" | "turnedOffFeatures" | "turnedOffTracks"> & {
+    msaFormat: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<import("msa-parsers").MSAFormat>>;
+}, "id" | "type" | "allowedGappyness" | "clades" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "drawMsaLetters" | "encodings" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "msaFilehandle" | "relativeTo" | "residueMappings" | "rowHeight" | "rowPanels" | "scrollX" | "scrollY" | "scrollZoom" | "scrollZoomAxis" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "trackHeights" | "treeFilehandle" | "treeMetadataFilehandle" | "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]>;
     showDomainLegend: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     hideGaps: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     allowedGappyness: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
     subFeatureRows: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-    type: import("@jbrowse/mobx-state-tree").ISimpleType<"MsaView">;
+    type: import("@jbrowse/mobx-state-tree").ILiteralType<"MsaView">;
     drawMsaLetters: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     scrollZoom: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    scrollZoomAxis: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<"both" | "horizontal" | "vertical">, [undefined]>;
     height: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
     rowHeight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
     scrollY: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
@@ -520,6 +525,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     collapsed: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISimpleType<string>>, [undefined]>;
     showOnly: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     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").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<{
@@ -539,7 +545,10 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     relativeTo: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     highlightColumns: import("@jbrowse/mobx-state-tree").IType<number[] | undefined, number[] | undefined, number[] | undefined>;
     highlights: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("react-msaview").Highlight, import("react-msaview").Highlight, import("react-msaview").Highlight>>, [undefined]>;
-}, "init" | "querySeqName" | "querySeqOffset" | "zoomToBaseLevel" | "connectedViewId" | "connectedFeature" | "connectedTranscript" | "blastParams" | "orthologParams" | "uniprotId" | "dataStoreId" | "mafRegion"> & {
+    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").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" | "querySeqOffset" | "zoomToBaseLevel" | "launchCompleted" | "connectedViewId" | "connectedFeature" | "connectedTranscript" | "blastParams" | "orthologParams" | "uniprotId" | "dataStoreId" | "mafRegion" | "region"> & {
     connectedViewId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     connectedFeature: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
     connectedTranscript: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
@@ -551,14 +560,21 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     zoomToBaseLevel: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     init: import("@jbrowse/mobx-state-tree").IType<MsaViewInitState | undefined, MsaViewInitState | undefined, MsaViewInitState | undefined>;
     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>;
+    region: import("@jbrowse/mobx-state-tree").IType<Region | undefined, Region | undefined, Region | undefined>;
 }, {
     width: number;
+    bodyMounted: boolean;
 } & {
+    readonly effectiveBodyMounted: boolean;
     menuItems(): MenuItem[];
+    readonly ownTracks: import("@jbrowse/core/util").AbstractTrackModel[];
+    readonly ownViews: import("@jbrowse/core/util").AbstractViewModel[];
 } & {
     setDisplayName(name: string): void;
     setWidth(newWidth: number): void;
+    setBodyMounted(flag: boolean): void;
     setMinimized(flag: boolean): void;
 } & {
     queueOfDialogs: [import("@jbrowse/core/util").DialogComponentType, any][];
@@ -576,14 +592,18 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     setAutoTreeAreaWidth(arg: boolean): void;
     setShowBranchLen(arg: boolean): 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;
     setBgColor(arg: boolean): void;
     setShowColumnStats(arg: boolean): void;
-    setMSAFormat(arg?: import("react-msaview").MSAFormat): void;
+    setMSAFormat(arg?: import("msa-parsers").MSAFormat): void;
 } & {
     headerHeight: number;
+    hideHeader: boolean;
     status: {
         msg: string;
         onCancel?: () => void;
@@ -605,16 +625,12 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     highlightedColumns: number[] | undefined;
     transientHighlights: Record<string, import("react-msaview").Highlight[]>;
     minimapHeight: number;
-    conservationTrackHeight: number;
-    columnTrackHeights: Record<string, number>;
-    sequenceLogoTrackHeight: number;
-    arcTrackHeight: number;
     marginLeft: number;
     error: unknown;
     warnings: string[];
     resetCount: number;
     hostCarriesData: boolean;
-    annotations: import("react-msaview").Annotation[];
+    annotations: import("msa-parsers").Annotation[];
 } & {
     drawRelativeTo(id: string | undefined): void;
     setHideGaps(arg: boolean): void;
@@ -631,6 +647,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     setMousePos(col?: number, row?: number): void;
     setHighlightedColumns(columns?: number[]): void;
     setHighlights(highlights: import("react-msaview").Highlight[]): void;
+    setClades(clades: import("react-msaview").Clade[]): void;
     applyHighlight(owner: string, highlights: import("react-msaview").Highlight[]): void;
     clearHighlight(owner: string): void;
     setShowDomains(arg: boolean): void;
@@ -682,12 +699,16 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     readonly noDomains: boolean;
     readonly unshareableData: import("react-msaview").UnshareableData[];
     menuItems(): never[];
-    readonly treeMetadata: Record<string, Record<string, string> | undefined>;
-    readonly MSA: import("react-msaview").MSAParserType | null;
+    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 numColumns: number;
     readonly tree: import("react-msaview").NodeWithIds;
     readonly rowNames: string[];
     readonly rowNamesSet: Map<string, number>;
+    readonly resolvedClades: import("react-msaview").ResolvedClade[];
+    readonly cladeGutterWidth: number;
     readonly mouseOverRowName: string | undefined;
     readonly hoveredInsertion: {
         rowName: string;
@@ -695,6 +716,21 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
         letters: string;
     } | undefined;
     readonly root: import("react-msaview").HierarchyNode<import("react-msaview").NodeWithIds>;
+    readonly treeOverviewHeight: number;
+    readonly treeOverviewLayout: {
+        root: import("react-msaview").HierarchyNode<import("react-msaview").NodeWithIds>;
+        numTips: number;
+        maxDepthToLeaf: number;
+        showBranchLen: boolean;
+    } | undefined;
+    readonly treeOverviewClades: import("react-msaview").ResolvedClade[];
+    readonly treeOverviewFocusRows: [number, number] | undefined;
+    treeOverviewHit(y: number): {
+        id: string;
+        rows: [number, number];
+    } | undefined;
+    readonly rowPanelsWidth: number;
+    readonly rowPanelsHeaderHeight: 0 | 56;
     readonly msaAreaWidth: number;
     readonly treeAreaWidthMinusMargin: number;
     readonly blanks: number[];
@@ -733,6 +769,15 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
 } & {
     readonly showMsaLetters: boolean;
     readonly showTreeText: boolean;
+} & {
+    readonly columnTrackContent: Map<string, {
+        values?: number[];
+        data?: string;
+        arcs?: import("react-msaview").Arc[];
+    }>;
+    trackHeight(kind: import("react-msaview").TrackKind, heightKey?: string, given?: number): number;
+    columnTrackModel(track: import("react-msaview").ColumnTrackSpec): import("react-msaview").BasicTrack;
+    readonly columnTrackModels: import("react-msaview").BasicTrack[];
 } & {
     readonly labelWidthMap: Map<string, number>;
     readonly labelWidthScale: number;
@@ -741,12 +786,6 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     readonly seqConsensus: string | undefined;
     readonly secondaryStructureArcs: import("react-msaview").Arc[] | undefined;
     readonly adapterTrackModels: import("react-msaview").BasicTrack[];
-    readonly columnTrackContent: Map<string, {
-        values?: number[];
-        data?: string;
-        arcs?: import("react-msaview").Arc[];
-    }>;
-    readonly columnTrackModels: import("react-msaview").BasicTrack[];
     readonly basePairTrackModels: import("react-msaview").BasicTrack[];
     readonly computedTrackModels: import("react-msaview").BasicTrack[];
     readonly tracks: import("react-msaview").BasicTrack[];
@@ -759,6 +798,10 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     visibleColToGlobalCol(visibleCol: number): number;
     seqPosToGlobalCol(rowName: string, seqPos: number): number | undefined;
     seqPosToVisibleCol(rowName: string, seqPos: number): number | undefined;
+    visibleSpan({ row, start: rawStart, end: rawEnd }: Region): {
+        startCol: number;
+        endCol: number;
+    } | undefined;
     readonly residueMappingProblems: import("react-msaview").ResidueMappingProblem[];
     readonly usableResidueMappings: import("react-msaview").ResidueMapping[];
     readonly mappedStructures: {
@@ -768,11 +811,17 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     structureResidue(rowName: string, seqPos: number, structureId?: string): import("react-msaview").StructureResidue | undefined;
     rowResidue(structureId: string, position: number, asymId?: string): import("react-msaview").RowResidue | undefined;
 } & {
+    readonly treeScaleBar: {
+        step: number;
+        px: number;
+        label: string;
+    } | undefined;
+    readonly topBandHeight: number;
     readonly msaAreaHeight: number;
     readonly totalTrackAreaHeight: number;
-    readonly annotationTypes: Map<string, import("react-msaview").Annotation>;
-    readonly filteredAnnotations: import("react-msaview").Annotation[];
-    readonly annotationsByRow: Record<string, import("react-msaview").Annotation[]>;
+    readonly annotationTypes: Map<string, import("msa-parsers").Annotation>;
+    readonly filteredAnnotations: import("msa-parsers").Annotation[];
+    readonly annotationsByRow: Record<string, import("msa-parsers").Annotation[]>;
 } & {
     readonly showVerticalScrollbar: boolean;
 } & {
@@ -784,9 +833,11 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     readonly isLoading: boolean;
     readonly maxScrollX: number;
     readonly maxScrollY: number;
+    readonly wheelZoomAxis: "both" | "horizontal" | "vertical";
 } & {
     setDrawMsaLetters(arg: boolean): void;
     setScrollZoom(arg: boolean): void;
+    setScrollZoomAxis(arg: "both" | "horizontal" | "vertical"): void;
     setHoveredTreeNode(nodeId?: string): void;
     calculateNeighborJoiningTreeFromMSA(): void;
     replaceTree(newick: string): void;
@@ -797,15 +848,18 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     zoomOutVertical(): void;
     zoomIn(): void;
     zoomOut(): void;
-    zoomToPos(scaleFactor: number, offsetX: number, offsetY: number): void;
+    zoomToPos(scaleFactor: number, offsetX: number, offsetY: number, axis?: "both" | "horizontal" | "vertical"): void;
     doScrollY(deltaY: number): void;
     setScrollY(n: number): void;
-    setAnnotations(annotations: import("react-msaview").Annotation[]): void;
-    setDomains(data?: Record<string, import("react-msaview").InterProScanResults>): void;
+    setAnnotations(annotations: import("msa-parsers").Annotation[]): void;
+    setDomains(data?: Record<string, import("msa-parsers").InterProScanResults>): void;
     applyGFFText(gffText: string): void;
     doScrollX(deltaX: number): void;
     setScrollX(n: number): void;
     setColumnTracks(tracks: import("react-msaview").ColumnTrackSpec[]): void;
+    setRowData(rowData: Record<string, Record<string, string>>): 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;
     setStatus(status?: {
@@ -815,19 +869,28 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
 } & {
     readonly verticalScrollbarWidth: 0 | 20;
     readonly msaCanvasWidth: number;
-    readonly segmentDomainTypes: import("react-msaview").Annotation[];
-    readonly categoricalDomainTypes: import("react-msaview").Annotation[];
+    cellAt(visibleCol: number, rowIndex?: number): import("react-msaview").Cell;
+    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 fillPalette: {
         [x: string]: string;
     };
-    readonly strokePalette: {
-        [k: string]: string;
-    };
+    readonly featureFillEncoding: import("react-msaview").ResolvedEncoding | undefined;
+    readonly featureColors: Map<import("msa-parsers").Annotation, {
+        fill: string;
+        stroke: string;
+    }>;
+    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: {
@@ -835,37 +898,32 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
         end: number;
     }[];
     readonly resolvedHighlights: import("react-msaview").ResolvedHighlight[];
-    readonly mouseOverColumnStats: {
-        col: number;
-        total: number;
-        gaps: number;
-        gapFraction: number;
-        conservation: number;
-        propertyConservation: number | undefined;
-        consensusLetter: string;
-        consensusCount: number;
-        consensusFraction: number;
-        distribution: [string, number][];
-    } | undefined;
+    columnStatsAt(col: number): import("react-msaview").ColumnStats | undefined;
     getRowData(name: string): {
         data: {
             name?: string;
             accession?: string;
             dbxref?: string;
         } | undefined;
-        treeMetadata: Record<string, string> | undefined;
+        rowData: Record<string, string> | undefined;
     };
+    readonly resolvedEncodings: import("react-msaview").ResolvedEncoding[];
+    readonly resolvedRowPanels: import("react-msaview").ResolvedRowPanel[];
+    readonly featureAlignShifts: Map<string, Map<string, number>>;
+    readonly tipLabelColors: Map<string, string> | undefined;
+    readonly rowTints: (string | undefined)[] | undefined;
+    readonly branchColors: Map<string, string> | undefined;
 } & {
     setHeaderHeight(arg: number): void;
-    setConservationTrackHeight(arg: number): void;
-    setColumnTrackHeight(id: string, height: number): void;
-    setSequenceLogoTrackHeight(arg: number): void;
-    setArcTrackHeight(arg: number): void;
+    setHideHeader(arg: boolean): void;
+    treeOverviewClick(y: number): void;
+    setTrackHeight(heightKey: string, height: number): void;
     reset(): void;
     exportSVG(opts: import("react-msaview").ExportSvgOptions): Promise<void>;
     setFilter(accession: string, shown: boolean): void;
     fit(): void;
     fitVertically(): void;
+    zoomToRegion(region: Region): void;
     fitHorizontally(): void;
     afterCreate(): void;
 } & {
@@ -911,6 +969,19 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
      * to draw the same highlights in its own display
      */
     readonly connectedHighlights: IRegion[];
+} & {
+    /**
+     * #getter
+     * overrides base
+     *
+     * react-msaview drops any snapshot document over 50kb and warns that a
+     * link to the view opens without it. True for an alignment this browser
+     * is holding in IndexedDB; wrong for an indexed view, whose kept `init`
+     * names a bgzip block over HTTP that processInit refetches wherever the
+     * session is opened -- so that one showed "Not in the link" about an
+     * alignment the link does carry.
+     */
+    readonly hostRestoresData: boolean;
 } & {
     /**
      * #action
@@ -956,10 +1027,18 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
      * #action
      */
     setDataStoreId(arg?: string): void;
+    /**
+     * #action
+     */
+    setLaunchCompleted(arg: boolean): void;
     /**
      * #action
      */
     setMafRegion(arg?: MafRegion): void;
+    /**
+     * #action
+     */
+    setRegion(arg?: Region): void;
     /**
      * #action
      */
@@ -988,9 +1067,13 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     cancelLaunch(): void;
     /**
      * #action
-     * Run the failed request again. The request IS the params, so re-stating
-     * them is the whole retry: each is a frozen property, and a fresh object
-     * is a change the launch autoruns wake on.
+     * Run the request again. The request IS the params, so re-stating them is
+     * the whole retry: each is a frozen property, and a fresh object is a
+     * change the launch autoruns wake on.
+     *
+     * A launch that already succeeded keeps its params and is marked
+     * `launchCompleted`, so clearing that mark is the whole retry for a view
+     * whose stored alignment expired.
      */
     retryLaunch(): void;
     /**
@@ -1028,15 +1111,11 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     menuItems(): MenuItem[];
 } & {
     afterCreate(): void;
-}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
-    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").IType<boolean | undefined, boolean, boolean>;
-}> & (({
+}, import("@jbrowse/mobx-state-tree")._NotCustomized, ({
     bgColor: boolean;
     colorSchemeName: string;
     showColumnStats: boolean;
-    msaFormat: import("react-msaview").MSAFormat | undefined;
+    msaFormat: import("msa-parsers").MSAFormat | undefined;
     drawLabels: boolean;
     labelsAlignRight: boolean;
     treeAreaWidth: number;
@@ -1044,6 +1123,9 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     showBranchLen: boolean;
     drawTree: boolean;
     drawNodeBubbles: boolean;
+    drawNodeLabels: boolean;
+    showTreeOverview: boolean;
+    overviewHeight: number;
     autoTreeAreaWidth: boolean;
     columnTracks: import("react-msaview").ColumnTrackSpec[];
     id: string;
@@ -1055,6 +1137,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     type: "MsaView";
     drawMsaLetters: boolean;
     scrollZoom: boolean;
+    scrollZoomAxis: "both" | "horizontal" | "vertical";
     height: number;
     rowHeight: number;
     scrollY: number;
@@ -1144,11 +1227,15 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     collapsed: string[];
     showOnly: string | undefined;
     turnedOffTracks: import("mobx").IKeyValueMap<boolean>;
+    trackHeights: import("mobx").IKeyValueMap<number>;
     residueMappings: import("react-msaview").ResidueMapping[];
     turnedOffFeatures: import("mobx").IKeyValueMap<boolean>;
     relativeTo: string | undefined;
     highlightColumns: number[] | undefined;
     highlights: import("react-msaview").Highlight[];
+    clades: import("react-msaview").Clade[];
+    encodings: import("react-msaview").Encoding[];
+    rowPanels: import("react-msaview").RowPanelSpec[];
     data: {
         tree?: string | undefined;
         msa?: string | undefined;
@@ -1159,7 +1246,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     bgColor: boolean;
     colorSchemeName: string;
     showColumnStats: boolean;
-    msaFormat: import("react-msaview").MSAFormat | undefined;
+    msaFormat: import("msa-parsers").MSAFormat | undefined;
     drawLabels: boolean;
     labelsAlignRight: boolean;
     treeAreaWidth: number;
@@ -1167,6 +1254,9 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     showBranchLen: boolean;
     drawTree: boolean;
     drawNodeBubbles: boolean;
+    drawNodeLabels: boolean;
+    showTreeOverview: boolean;
+    overviewHeight: number;
     autoTreeAreaWidth: boolean;
     columnTracks?: undefined;
     id: string;
@@ -1178,6 +1268,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     type: "MsaView";
     drawMsaLetters: boolean;
     scrollZoom: boolean;
+    scrollZoomAxis: "both" | "horizontal" | "vertical";
     height: number;
     rowHeight: number;
     scrollY: number;
@@ -1267,18 +1358,22 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     collapsed: string[];
     showOnly: string | undefined;
     turnedOffTracks: import("mobx").IKeyValueMap<boolean>;
+    trackHeights: import("mobx").IKeyValueMap<number>;
     residueMappings: import("react-msaview").ResidueMapping[];
     turnedOffFeatures: import("mobx").IKeyValueMap<boolean>;
     relativeTo: string | undefined;
     highlightColumns: number[] | undefined;
     highlights: import("react-msaview").Highlight[];
+    clades: import("react-msaview").Clade[];
+    encodings: import("react-msaview").Encoding[];
+    rowPanels: import("react-msaview").RowPanelSpec[];
     data: {
         tree?: string | undefined;
         msa?: string | undefined;
         treeMetadata?: string | undefined;
         gff?: string | undefined;
     };
-} & import("@jbrowse/mobx-state-tree")._NotCustomized))>;
+} & import("@jbrowse/mobx-state-tree")._NotCustomized)>;
 export type JBrowsePluginMsaViewStateModel = ReturnType<typeof stateModelFactory>;
 export type JBrowsePluginMsaViewModel = Instance<JBrowsePluginMsaViewStateModel>;
 export { type MafRegion, type MsaViewInitState } from './types';

package/dist/MsaViewPanel/model.js

@@ -5,6 +5,7 @@ import { genomeToTranscriptSeqMapping } from 'g2p_mapper';
 import { autorun } from 'mobx';
 import { MSAModelF } from 'react-msaview';
 import { autoLoadProteinDomains, launchBlastIfNeeded, launchOrthologsIfNeeded, loadStoredData, observeProteinHighlights, processInit, runCleanup, storeDataToIndexedDB, syncGenomeHoverToMsaColumn, } from './afterCreateAutoruns';
+import { applyRegion } from './applyRegion';
 import { msaCoordToGenomeCoord, msaCoordToGenomeRegions, } from './msaCoordToGenomeCoord';
 import { deleteMsaData } from './msaDataStore';
 import { resolveConnectedTranscriptIfNeeded } from './resolveConnectedTranscript';
@@ -86,10 +87,34 @@ export default function stateModelFactory() {
          * #property
          */
         dataStoreId: types.maybe(types.string),
+        /**
+         * #property
+         * whether the request above has already produced this view's alignment.
+         *
+         * The params used to be cleared to mark that, which threw away the only
+         * statement of what the view is: browser storage expires an alignment
+         * after 7 days, and the view could then only tell the user to start
+         * over from the gene. A flag says the same thing and duplicates
+         * nothing, where a kept copy of the request put a second protein
+         * sequence and a second exon model in every saved session.
+         *
+         * A snapshot property rather than a volatile, because the case it
+         * exists for is by construction a later session: expiry is discovered
+         * by `loadStoredData` on restore, and a volatile would be false there
+         * and refire the whole search unasked.
+         */
+        launchCompleted: false,
         /**
          * #property
          */
         mafRegion: types.frozen(),
+        /**
+         * #property
+         * where the view opens: 1-based residues of `row`, or alignment
+         * columns without one. Zoomed onto once and then cleared, so a
+         * reloaded session keeps the reader's own scroll.
+         */
+        region: types.frozen(),
     }))
         .volatile(() => ({
         /**
@@ -182,6 +207,26 @@ export default function stateModelFactory() {
                 ...this.connectedClickHighlights,
             ];
         },
+    }))
+        .views(self => ({
+        /**
+         * #getter
+         * overrides base
+         *
+         * react-msaview drops any snapshot document over 50kb and warns that a
+         * link to the view opens without it. True for an alignment this browser
+         * is holding in IndexedDB; wrong for an indexed view, whose kept `init`
+         * names a bgzip block over HTTP that processInit refetches wherever the
+         * session is opened -- so that one showed "Not in the link" about an
+         * alignment the link does carry.
+         */
+        get hostRestoresData() {
+            const { msaIndexedLocation, msaName } = self.init ?? {};
+            // `hostCarriesData` first: it is the base answer, the volatile a simple
+            // host flips, and overriding the getter without it threw that switch
+            // away for every view this one does not speak for
+            return self.hostCarriesData || !!(msaIndexedLocation && msaName);
+        },
     }))
         .actions(self => ({
         /**
@@ -250,12 +295,24 @@ export default function stateModelFactory() {
         setDataStoreId(arg) {
             self.dataStoreId = arg;
         },
+        /**
+         * #action
+         */
+        setLaunchCompleted(arg) {
+            self.launchCompleted = arg;
+        },
         /**
          * #action
          */
         setMafRegion(arg) {
             self.mafRegion = arg;
         },
+        /**
+         * #action
+         */
+        setRegion(arg) {
+            self.region = arg;
+        },
         /**
          * #action
          */
@@ -295,15 +352,20 @@ export default function stateModelFactory() {
             self.blastParams = undefined;
             self.orthologParams = undefined;
             self.init = undefined;
+            self.launchCompleted = false;
             self.progress = '';
             self.rid = undefined;
             self.error = undefined;
         },
         /**
          * #action
-         * Run the failed request again. The request IS the params, so re-stating
-         * them is the whole retry: each is a frozen property, and a fresh object
-         * is a change the launch autoruns wake on.
+         * Run the request again. The request IS the params, so re-stating them is
+         * the whole retry: each is a frozen property, and a fresh object is a
+         * change the launch autoruns wake on.
+         *
+         * A launch that already succeeded keeps its params and is marked
+         * `launchCompleted`, so clearing that mark is the whole retry for a view
+         * whose stored alignment expired.
          */
         retryLaunch() {
             self.launchController?.abort();
@@ -311,6 +373,7 @@ export default function stateModelFactory() {
             self.progress = '';
             self.rid = undefined;
             self.error = undefined;
+            self.launchCompleted = false;
             if (self.blastParams) {
                 self.blastParams = { ...self.blastParams };
             }
@@ -444,6 +507,9 @@ export default function stateModelFactory() {
             // so they're factories returning the autorun body rather than plain fns
             addDisposer(self, autorun(syncGenomeHoverToMsaColumn(self)));
             addDisposer(self, autorun(observeProteinHighlights(self)));
+            addDisposer(self, autorun(() => {
+                applyRegion(self);
+            }));
         },
     }));
 }