jbrowse-plugin-msaview 3.4.0 → 3.5.0

package/dist/MsaViewPanel/model.d.ts

@@ -1,7 +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;
@@ -22,8 +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';
@@ -37,17 +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.
@@ -65,7 +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
@@ -85,7 +111,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     displayName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     minimized: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-}, "id" | "type" | "autoTreeAreaWidth" | "drawLabels" | "drawNodeBubbles" | "drawTree" | "labelsAlignRight" | "showBranchLen" | "treeAreaWidth" | "treeWidth" | "bgColor" | "colorSchemeName" | "msaFormat" | "showColumnStats" | "allowedGappyness" | "colWidth" | "collapsed" | "currentAlignment" | "data" | "drawMsaLetters" | "featureFilters" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "msaFilehandle" | "relativeTo" | "rowHeight" | "scrollX" | "scrollY" | "scrollZoom" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "treeFilehandle" | "treeMetadataFilehandle" | "turnedOffTracks"> & Omit<Omit<Omit<{}, "autoTreeAreaWidth" | "drawLabels" | "drawNodeBubbles" | "drawTree" | "labelsAlignRight" | "showBranchLen" | "treeAreaWidth" | "treeWidth"> & {
+}, "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"> & {
     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]>;
@@ -98,8 +124,8 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     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" | "currentAlignment" | "data" | "drawMsaLetters" | "featureFilters" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "msaFilehandle" | "relativeTo" | "rowHeight" | "scrollX" | "scrollY" | "scrollZoom" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "treeFilehandle" | "treeMetadataFilehandle" | "turnedOffTracks"> & {
+    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"> & {
     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]>;
@@ -494,6 +520,8 @@ 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]>;
+    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>>;
@@ -507,15 +535,18 @@ 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>;
-}, "init" | "querySeqName" | "zoomToBaseLevel" | "connectedViewId" | "connectedFeature" | "blastParams" | "orthologParams" | "uniprotId" | "dataStoreId" | "mafRegion"> & {
+    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"> & {
     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>;
@@ -524,7 +555,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
 }, {
     width: number;
 } & {
-    menuItems(): import("@jbrowse/core/ui").MenuItem[];
+    menuItems(): MenuItem[];
 } & {
     setDisplayName(name: string): void;
     setWidth(newWidth: number): void;
@@ -550,12 +581,11 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     setColorSchemeName(name: 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;
     status: {
         msg: string;
-        url?: string;
         onCancel?: () => void;
     } | undefined;
     highResScaleFactor: number;
@@ -573,12 +603,18 @@ 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;
+    columnTrackHeights: Record<string, number>;
     sequenceLogoTrackHeight: number;
+    arcTrackHeight: number;
     marginLeft: number;
     error: unknown;
-    annotations: import("msa-parsers").Annotation[];
+    warnings: string[];
+    resetCount: number;
+    hostCarriesData: boolean;
+    annotations: import("react-msaview").Annotation[];
 } & {
     drawRelativeTo(id: string | undefined): void;
     setHideGaps(arg: boolean): void;
@@ -589,8 +625,14 @@ 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;
+    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;
@@ -608,18 +650,20 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     }): void;
     setMSAFilehandle(msaFilehandle?: import("@jbrowse/core/util").FileLocation): void;
     setTreeFilehandle(treeFilehandle?: import("@jbrowse/core/util").FileLocation): void;
+    setTreeMetadataFilehandle(treeMetadataFilehandle?: import("@jbrowse/core/util").FileLocation): void;
     setGFFFilehandle(gffFilehandle?: import("@jbrowse/core/util").FileLocation): void;
     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;
@@ -636,9 +680,10 @@ 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 MSA: import("msa-parsers").MSAParserType | null;
+    readonly MSA: import("react-msaview").MSAParserType | null;
     readonly numColumns: number;
     readonly tree: import("react-msaview").NodeWithIds;
     readonly rowNames: string[];
@@ -659,7 +704,7 @@ 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[];
@@ -677,29 +722,74 @@ 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[];
+    }>;
+    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;
+    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 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 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;
 } & {
     setDrawMsaLetters(arg: boolean): void;
     setScrollZoom(arg: boolean): void;
     setHoveredTreeNode(nodeId?: string): void;
     calculateNeighborJoiningTreeFromMSA(): void;
+    replaceTree(newick: string): void;
     resetZoom(): void;
     zoomOutHorizontal(): void;
     zoomInHorizontal(): void;
@@ -710,46 +800,23 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     zoomToPos(scaleFactor: number, offsetX: number, offsetY: number): 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;
+    setDomains(data?: Record<string, import("react-msaview").InterProScanResults>): void;
     applyGFFText(gffText: string): void;
     doScrollX(deltaX: number): void;
     setScrollX(n: number): void;
+    setColumnTracks(tracks: import("react-msaview").ColumnTrackSpec[]): 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 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;
-    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;
     };
@@ -757,16 +824,17 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
         [k: string]: string;
     };
     readonly segmentLabels: Map<string, string>;
-    readonly visibleDomainTypes: import("msa-parsers").Annotation[];
+    readonly visibleDomainTypes: import("react-msaview").Annotation[];
     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: {
         start: number;
         end: number;
     }[];
+    readonly resolvedHighlights: import("react-msaview").ResolvedHighlight[];
     readonly mouseOverColumnStats: {
         col: number;
         total: number;
@@ -790,16 +858,12 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
 } & {
     setHeaderHeight(arg: number): void;
     setConservationTrackHeight(arg: number): void;
+    setColumnTrackHeight(id: string, height: number): void;
     setSequenceLogoTrackHeight(arg: number): void;
+    setArcTrackHeight(arg: number): void;
     reset(): void;
-    exportSVG(opts: {
-        theme: import("@mui/material").Theme;
-        includeMinimap?: boolean;
-        includeTracks?: boolean;
-        exportType: "entire" | "viewport";
-    }): Promise<void>;
-    initFilter(arg: string): void;
-    setFilter(arg: string, flag: boolean): void;
+    exportSVG(opts: import("react-msaview").ExportSvgOptions): Promise<void>;
+    setFilter(accession: string, shown: boolean): void;
     fit(): void;
     fitVertically(): void;
     fitHorizontally(): void;
@@ -807,19 +871,11 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
 } & {
     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
@@ -860,10 +916,6 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
      * #action
      */
     setZoomToBaseLevel(arg: boolean): void;
-    /**
-     * #action
-     */
-    setError(e: unknown): void;
     /**
      * #action
      */
@@ -876,6 +928,10 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
      * #action
      */
     setBlastParams(args?: BlastParams): void;
+    /**
+     * #action
+     */
+    setConnectedFeature(arg?: Record<string, unknown>): void;
     /**
      * #action
      */
@@ -888,6 +944,10 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
      * #action
      */
     setQuerySeqName(arg: string): void;
+    /**
+     * #action
+     */
+    setQuerySeqOffset(arg: number): void;
     /**
      * #action
      */
@@ -908,6 +968,31 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
      * #action
      */
     setIsStoringData(arg: boolean): void;
+    /**
+     * #action
+     */
+    setLastStoredData(arg?: MsaDataPayload): void;
+    /**
+     * #action
+     */
+    setLaunchController(arg?: AbortController): void;
+    /**
+     * #action
+     * 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 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.
+     */
+    retryLaunch(): void;
     /**
      * #action
      */
@@ -921,27 +1006,160 @@ 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>;
-}> & {
+}> & (({
+    bgColor: boolean;
+    colorSchemeName: string;
+    showColumnStats: boolean;
+    msaFormat: import("react-msaview").MSAFormat | undefined;
+    drawLabels: boolean;
+    labelsAlignRight: boolean;
+    treeAreaWidth: number;
+    treeWidth: number;
+    showBranchLen: boolean;
+    drawTree: boolean;
+    drawNodeBubbles: boolean;
+    autoTreeAreaWidth: boolean;
+    columnTracks: import("react-msaview").ColumnTrackSpec[];
+    id: string;
+    showDomains: boolean;
+    showDomainLegend: boolean;
+    hideGaps: boolean;
+    allowedGappyness: number;
+    subFeatureRows: boolean;
+    type: "MsaView";
+    drawMsaLetters: boolean;
+    scrollZoom: boolean;
+    height: number;
+    rowHeight: number;
+    scrollY: number;
+    scrollX: number;
+    colWidth: number;
+    treeFilehandle: import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | {
+        locationType: "UriLocation";
+        uri: string;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+            internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+            authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
+        }> | undefined;
+    } | undefined;
+    msaFilehandle: import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | {
+        locationType: "UriLocation";
+        uri: string;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+            internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+            authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
+        }> | undefined;
+    } | undefined;
+    treeMetadataFilehandle: import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | {
+        locationType: "UriLocation";
+        uri: string;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+            internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+            authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
+        }> | undefined;
+    } | undefined;
+    gffFilehandle: import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | {
+        locationType: "UriLocation";
+        uri: string;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+            internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+            authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
+        }> | undefined;
+    } | undefined;
+    currentAlignment: number;
+    collapsed: string[];
+    showOnly: string | undefined;
+    turnedOffTracks: import("mobx").IKeyValueMap<boolean>;
+    residueMappings: import("react-msaview").ResidueMapping[];
+    turnedOffFeatures: import("mobx").IKeyValueMap<boolean>;
+    relativeTo: string | undefined;
+    highlightColumns: number[] | undefined;
+    highlights: import("react-msaview").Highlight[];
+    data: {
+        tree?: string | undefined;
+        msa?: string | undefined;
+        treeMetadata?: string | undefined;
+        gff?: string | undefined;
+    };
+} & import("@jbrowse/mobx-state-tree")._NotCustomized) | ({
     bgColor: boolean;
     colorSchemeName: string;
     showColumnStats: boolean;
-    msaFormat: import("msa-parsers").MSAFormat | undefined;
+    msaFormat: import("react-msaview").MSAFormat | undefined;
     drawLabels: boolean;
     labelsAlignRight: boolean;
     treeAreaWidth: number;
@@ -950,6 +1168,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     drawTree: boolean;
     drawNodeBubbles: boolean;
     autoTreeAreaWidth: boolean;
+    columnTracks?: undefined;
     id: string;
     showDomains: boolean;
     showDomainLegend: boolean;
@@ -1048,16 +1267,18 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     collapsed: string[];
     showOnly: string | undefined;
     turnedOffTracks: import("mobx").IKeyValueMap<boolean>;
-    featureFilters: import("mobx").IKeyValueMap<boolean>;
+    residueMappings: import("react-msaview").ResidueMapping[];
+    turnedOffFeatures: import("mobx").IKeyValueMap<boolean>;
     relativeTo: string | undefined;
     highlightColumns: number[] | undefined;
+    highlights: import("react-msaview").Highlight[];
     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';