jbrowse-plugin-msaview 3.4.1 → 3.6.0

package/dist/MsaViewPanel/model.d.ts

@@ -1,8 +1,10 @@
 export type { MSAFormat } from 'msa-parsers';
 import type { BlastDatabase, MsaAlgorithm, PhmmerDatabase } from '../LaunchMsaView/components/BlastQuery/consts';
+import type { UnirefIdentity } from '../utils/unirefHomologs';
 import type { MsaDataPayload } from './msaDataStore';
 import type { MafRegion, MsaViewInitState } from './types';
-import type { Feature } from '@jbrowse/core/util';
+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';
 type LGV = LinearGenomeViewModel;
@@ -23,8 +25,19 @@ export interface IRegion {
  * orphan every row already written.
  */
 export type BlastParams = {
-    selectedTranscript?: Feature;
-    proteinSequence: string;
+    /** plain JSON, not a Feature: see TranscriptRef */
+    selectedTranscript?: TranscriptRef;
+    /**
+     * The query. The dialog always supplies it, translated from the transcript
+     * the user picked. A session spec may instead name a UniProt `accession`
+     * and have the sequence fetched at launch, or name a `connectedTranscript`
+     * on the view and have it translated from the genome (see
+     * resolveConnectedTranscript).
+     */
+    proteinSequence?: string;
+    accession?: string;
+    /** hits to keep: phmmer's `nhits`, blastp's `alignments`; 100 when omitted */
+    maxHits?: number;
 } & ({
     /** absent on params written before phmmer existed, which were all blastp */
     searchProgram?: 'blastp';
@@ -38,17 +51,28 @@ export type BlastParams = {
     msaAlgorithm?: undefined;
 });
 /**
- * Where the ortholog set comes from. NCBI's sets cover vertebrates and
+ * Where the homolog set comes from. NCBI's ortholog sets cover vertebrates and
  * insects; PANTHER's span its 144 reference proteomes, human to yeast to
- * Arabidopsis, so a gene from outside NCBI's scope aligns only through it.
+ * Arabidopsis; a UniRef cluster is every UniProtKB entry within 50% (or 90%)
+ * identity of the query, one per species, from any organism at all -- and the
+ * one source of the three whose rows need no ortholog call, only UniProt's
+ * REST api (see utils/unirefHomologs.ts).
  */
-export declare const orthologSources: readonly ["ncbi", "panther"];
+export declare const orthologSources: readonly ["ncbi", "panther", "uniref"];
 export type OrthologSource = (typeof orthologSources)[number];
 export interface OrthologParams {
     /** NCBI taxon id of the assembly the query gene came from */
     taxId: number;
     /** `ncbi` when omitted, so every launch written before this key keeps its meaning */
     source?: OrthologSource;
+    /** UniRef only: the cluster identity level, 50 when omitted */
+    identity?: UnirefIdentity;
+    /**
+     * UniRef only: keep members from reference proteomes, which is what makes a
+     * cluster one good entry per species rather than every strain and isolate
+     * UniProtKB holds. `true` when omitted.
+     */
+    referenceProteomesOnly?: boolean;
     /**
      * taxon ids to include as rows. The query taxon has its own row already, so
      * it is excluded from this set whether or not it is named.
@@ -66,7 +90,8 @@ export interface OrthologParams {
     /** candidate gene identifiers off the feature, tried in order */
     geneCandidates: string[];
     msaAlgorithm: MsaAlgorithm;
-    selectedTranscript?: Feature;
+    /** plain JSON, not a Feature: see TranscriptRef */
+    selectedTranscript?: TranscriptRef;
     /**
      * The query row, named `<species>_query`. The launch dialog always supplies
      * it, translated from the
@@ -85,8 +110,8 @@ 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" | "featureFilters" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "msaFilehandle" | "relativeTo" | "rowHeight" | "scrollX" | "scrollY" | "scrollZoom" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "treeFilehandle" | "treeMetadataFilehandle" | "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]>;
@@ -94,22 +119,26 @@ 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("msa-parsers").MSAFormat>>;
-}, "id" | "type" | "allowedGappyness" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "drawMsaLetters" | "featureFilters" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "msaFilehandle" | "relativeTo" | "rowHeight" | "scrollX" | "scrollY" | "scrollZoom" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "treeFilehandle" | "treeMetadataFilehandle" | "turnedOffTracks"> & {
+}, "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]>;
@@ -495,7 +524,9 @@ 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<{
         tree: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
         msa: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
@@ -509,28 +540,39 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     }, import("@jbrowse/mobx-state-tree")._NotCustomized, {
         [k: string]: string | undefined;
     }>, [undefined]>;
-    featureFilters: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>, [undefined]>;
+    turnedOffFeatures: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>, [undefined]>;
     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" | "zoomToBaseLevel" | "connectedViewId" | "connectedFeature" | "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"> & {
     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>>;
     blastParams: import("@jbrowse/mobx-state-tree").IType<BlastParams | undefined, BlastParams | undefined, BlastParams | undefined>;
     orthologParams: import("@jbrowse/mobx-state-tree").IType<OrthologParams | undefined, OrthologParams | undefined, OrthologParams | undefined>;
     querySeqName: import("@jbrowse/mobx-state-tree").IType<string | undefined, string, string>;
+    querySeqOffset: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
     uniprotId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     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>;
 }, {
     width: number;
+    bodyMounted: boolean;
 } & {
-    menuItems(): import("@jbrowse/core/ui").MenuItem[];
+    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][];
@@ -548,6 +590,9 @@ 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;
@@ -556,9 +601,9 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     setMSAFormat(arg?: import("msa-parsers").MSAFormat): void;
 } & {
     headerHeight: number;
+    hideHeader: boolean;
     status: {
         msg: string;
-        url?: string;
         onCancel?: () => void;
     } | undefined;
     highResScaleFactor: number;
@@ -576,11 +621,13 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
         descendantNames: string[];
     } | undefined;
     highlightedColumns: number[] | undefined;
+    transientHighlights: Record<string, import("react-msaview").Highlight[]>;
     minimapHeight: number;
-    conservationTrackHeight: number;
-    sequenceLogoTrackHeight: number;
     marginLeft: number;
     error: unknown;
+    warnings: string[];
+    resetCount: number;
+    hostCarriesData: boolean;
     annotations: import("msa-parsers").Annotation[];
 } & {
     drawRelativeTo(id: string | undefined): void;
@@ -592,9 +639,15 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     setHighResScaleFactor(arg: number): void;
     setHeight(height: number): void;
     setError(error?: unknown): void;
+    addWarning(warning: string): void;
+    clearWarnings(): void;
+    setHostCarriesData(arg: boolean): void;
     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;
     setShowDomainLegend(arg: boolean): void;
     setSubFeatureRows(arg: boolean): void;
@@ -617,14 +670,15 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     setMSA(result: string): void;
     setTree(result: string): void;
     setTreeMetadata(result: string): void;
+    setGFF(result: string): void;
 } & {
     readonly hideGapsEffective: boolean;
     readonly realAllowedGappyness: number;
     readonly actuallyShowDomains: boolean;
+    readonly hostRestoresData: boolean;
     readonly viewInitialized: boolean;
     readonly width: number;
 } & {
-    extraViewMenuItems(): never[];
     readonly colorScheme: Record<string, string>;
     readonly header: Record<string, unknown> | {
         info: string;
@@ -641,13 +695,18 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     readonly alignmentNames: string[];
     readonly noTree: boolean;
     readonly noDomains: boolean;
+    readonly unshareableData: import("react-msaview").UnshareableData[];
     menuItems(): never[];
-    readonly treeMetadata: Record<string, Record<string, string> | undefined>;
+    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;
@@ -655,6 +714,21 @@ 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[];
@@ -664,7 +738,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     }[]>;
     readonly rows: [string, string][];
     readonly numRows: number;
-    readonly seqPosGlobalColIndex: Map<string, Int32Array<ArrayBuffer>>;
+    seqPosIndex(rowName: string): Int32Array | undefined;
     readonly rowMap: Map<string, string>;
     readonly columns: Map<string, string>;
     readonly columns2d: string[];
@@ -682,29 +756,87 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     readonly hierarchy: import("react-msaview").HierarchyNode<import("react-msaview").NodeWithIdsAndLength>;
     readonly totalHeight: number;
     readonly leaves: import("react-msaview").HierarchyNode<import("react-msaview").NodeWithIdsAndLength>[];
+    readonly rootToTipLength: number;
     readonly maxBranchLength: number;
+    readonly pxPerBranchLength: number;
     readonly maxDepthToLeaf: number;
     readonly allBranchesLength0: boolean;
     readonly showBranchLenEffective: boolean;
 } & {
     readonly totalWidth: number;
+} & {
+    readonly showMsaLetters: boolean;
+    readonly showTreeText: boolean;
+} & {
+    readonly labelWidthMap: Map<string, number>;
+    readonly labelWidthScale: number;
+    readonly labelsWidth: number;
+    readonly secondaryStructureConsensus: string | undefined;
+    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[];
+    }>;
+    trackHeight(kind: import("react-msaview").TrackKind, heightKey?: string, given?: number): number;
+    readonly columnTrackModels: import("react-msaview").BasicTrack[];
+    readonly basePairTrackModels: import("react-msaview").BasicTrack[];
+    readonly computedTrackModels: import("react-msaview").BasicTrack[];
+    readonly tracks: import("react-msaview").BasicTrack[];
+    readonly turnedOnTracks: import("react-msaview").BasicTrack[];
+    readonly showHorizontalScrollbar: boolean;
+    visibleColToRowLetter(rowName: string, visibleCol: number): string | undefined;
+    visibleColToSeqPos(rowName: string, visibleCol: number): number | undefined;
+    visibleColToSeqPosOneBased(rowName: string, visibleCol: number): number | undefined;
+    globalColToVisibleCol(globalCol: number): number | undefined;
+    visibleColToGlobalCol(visibleCol: number): number;
+    seqPosToGlobalCol(rowName: string, seqPos: number): number | undefined;
+    seqPosToVisibleCol(rowName: string, seqPos: number): number | undefined;
+    visibleSpan({ row, start: rawStart, end: rawEnd }: import("react-msaview").Region): {
+        startCol: number;
+        endCol: number;
+    } | undefined;
+    readonly residueMappingProblems: import("react-msaview").ResidueMappingProblem[];
+    readonly usableResidueMappings: import("react-msaview").ResidueMapping[];
+    readonly mappedStructures: {
+        row: string;
+        structure: import("react-msaview").MappedStructure;
+    }[];
+    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("msa-parsers").Annotation>;
+    readonly filteredAnnotations: import("msa-parsers").Annotation[];
+    readonly annotationsByRow: Record<string, import("msa-parsers").Annotation[]>;
+} & {
+    readonly showVerticalScrollbar: boolean;
 } & {
     readonly dataInitialized: boolean;
     readonly blocksX: number[];
     readonly blocksY: number[];
-    readonly visibleMsaHeight: number;
 } & {
     readonly blocks2d: (readonly [number, number])[];
     readonly isLoading: boolean;
     readonly maxScrollX: number;
     readonly maxScrollY: number;
-    readonly showMsaLetters: boolean;
-    readonly showTreeText: boolean;
+    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;
     resetZoom(): void;
     zoomOutHorizontal(): void;
     zoomInHorizontal(): void;
@@ -712,7 +844,7 @@ 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("msa-parsers").Annotation[]): void;
@@ -721,44 +853,22 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     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?: {
         msg: string;
-        url?: string;
         onCancel?: () => void;
     }): void;
-} & {
-    readonly labelWidthMap: Map<string, number>;
-    readonly labelWidthScale: number;
-    readonly labelsWidth: number;
-    readonly secondaryStructureConsensus: string | undefined;
-    readonly seqConsensus: string | undefined;
-    readonly adapterTrackModels: import("react-msaview").BasicTrack[];
-    readonly columnTrackContent: Map<string, {
-        values?: number[];
-        data?: string;
-    }>;
-    readonly columnTrackModels: import("react-msaview").BasicTrack[];
-    readonly tracks: import("react-msaview").BasicTrack[];
-    readonly turnedOnTracks: import("react-msaview").BasicTrack[];
-    readonly showHorizontalScrollbar: boolean;
-    visibleColToRowLetter(rowName: string, visibleCol: number): string | undefined;
-    visibleColToSeqPos(rowName: string, visibleCol: number): number | undefined;
-    visibleColToSeqPosOneBased(rowName: string, visibleCol: number): number | undefined;
-    globalColToVisibleCol(globalCol: number): number | undefined;
-    seqPosToGlobalCol(rowName: string, seqPos: number): number;
-    seqPosToVisibleCol(rowName: string, seqPos: number): number | undefined;
-} & {
-    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 showVerticalScrollbar: boolean;
 } & {
     readonly verticalScrollbarWidth: 0 | 20;
     readonly msaCanvasWidth: number;
+    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: {
@@ -767,8 +877,16 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     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("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("msa-parsers").Annotation[];
@@ -779,56 +897,43 @@ 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;
+    readonly mouseOverColumnStats: 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;
-    setSequenceLogoTrackHeight(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>;
-    initFilter(arg: string): void;
-    setFilter(arg: string, flag: boolean): void;
+    setFilter(accession: string, shown: boolean): void;
     fit(): void;
     fitVertically(): void;
+    zoomToRegion(region: import("react-msaview").Region): void;
     fitHorizontally(): void;
     afterCreate(): void;
 } & {
     rid: string | undefined;
     progress: string;
-    error: unknown;
     loadingStoredData: boolean;
     isStoringData: boolean;
     lastStoredData: MsaDataPayload | undefined;
     launchController: AbortController | undefined;
     domainsRequested: boolean;
-} & {
-    /**
-     * #method
-     */
-    getRowByName(rowName: string): [string, string] | undefined;
-    /**
-     * #method
-     */
-    getSequenceByRowName(rowName: string): string | undefined;
 } & {
     /**
      * #getter
@@ -866,13 +971,22 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     readonly connectedHighlights: IRegion[];
 } & {
     /**
-     * #action
+     * #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.
      */
-    setZoomToBaseLevel(arg: boolean): void;
+    readonly hostRestoresData: boolean;
+} & {
     /**
      * #action
      */
-    setError(e: unknown): void;
+    setZoomToBaseLevel(arg: boolean): void;
     /**
      * #action
      */
@@ -885,6 +999,10 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
      * #action
      */
     setBlastParams(args?: BlastParams): void;
+    /**
+     * #action
+     */
+    setConnectedFeature(arg?: Record<string, unknown>): void;
     /**
      * #action
      */
@@ -897,6 +1015,10 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
      * #action
      */
     setQuerySeqName(arg: string): void;
+    /**
+     * #action
+     */
+    setQuerySeqOffset(arg: number): void;
     /**
      * #action
      */
@@ -905,6 +1027,10 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
      * #action
      */
     setDataStoreId(arg?: string): void;
+    /**
+     * #action
+     */
+    setLaunchCompleted(arg: boolean): void;
     /**
      * #action
      */
@@ -927,13 +1053,25 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     setLaunchController(arg?: AbortController): void;
     /**
      * #action
-     * Abandon the launch in flight. The EBI job keeps running on their side —
-     * nothing here can recall it, and its JobLink stays valid — so this only
-     * stops the polling and the writes it would make. Dropping the params is
-     * what keeps the request from refiring; the view falls back to the import
-     * form, which is where react-msaview's own cancel leaves it too.
+     * Abandon the launch, in flight or failed. The EBI job keeps running on
+     * their side — nothing here can recall it, and its JobLink stays valid —
+     * so this only stops the polling and the writes it would make. Dropping
+     * the request (the params, or the init) is what keeps it from refiring on
+     * the next reload; the view falls back to the import form, which is where
+     * react-msaview's own cancel leaves it too.
      */
     cancelLaunch(): void;
+    /**
+     * #action
+     * 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;
     /**
      * #action
      */
@@ -947,23 +1085,29 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
      * #action
      */
     setMouseClickPos(col?: number, row?: number): void;
+} & {
+    /**
+     * #action
+     * overrides base
+     *
+     * react-msaview's reset applies a snapshot filtered to its own
+     * `preservedOnReset` list, and a downstream property is never on it:
+     * returning to the import form dropped the view's name, un-minimized
+     * it, and forgot the zoom-on-click preference. The volatiles fail the
+     * other way -- applySnapshot cannot reach them, so the last file's
+     * state carried into the next one and the domain auto-load, which fires
+     * once per view, never fired again.
+     */
+    reset(): void;
 } & {
     /**
      * #method
+     * overrides base
      */
-    extraViewMenuItems(): {
-        label: string;
-        checked: boolean;
-        type: string;
-        onClick: () => void;
-    }[];
+    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;
@@ -975,6 +1119,9 @@ 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;
@@ -986,6 +1133,7 @@ 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;
@@ -1075,10 +1223,15 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     collapsed: string[];
     showOnly: string | undefined;
     turnedOffTracks: import("mobx").IKeyValueMap<boolean>;
-    featureFilters: 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;
@@ -1097,6 +1250,9 @@ 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;
@@ -1108,6 +1264,7 @@ 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;
@@ -1197,17 +1354,22 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     collapsed: string[];
     showOnly: string | undefined;
     turnedOffTracks: import("mobx").IKeyValueMap<boolean>;
-    featureFilters: 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';