jbrowse-plugin-msaview 5.16.1 → 5.17.0

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

@@ -28,11 +28,18 @@ const PreLoadedMSA = observer(function ({ model, feature, handleClose, preferred
     const { classes } = useStyles();
     const { pluginManager } = getEnv(model);
     const { assemblyNames } = view;
+    const assemblyName = assemblyNames[0];
     const { launchError, submit } = useLaunchSubmit(handleClose);
     const datasets = readMsaDatasets(session.jbrowse);
     const [selectedDatasetId, setSelectedDatasetId] = useState(datasets?.[0]?.datasetId);
     const selectedDataset = datasets?.find(d => d.datasetId === selectedDatasetId);
-    const { data: msaList, isLoading: msaListLoading, error: msaListFetchError, } = useFetch(selectedDataset ? `${selectedDataset.datasetId}-msa-list` : null, () => fetchMSAList({ config: selectedDataset.adapter, pluginManager }));
+    const { data: msaList, isLoading: msaListLoading, error: msaListFetchError, } = useFetch(selectedDataset
+        ? `${selectedDataset.datasetId}-${assemblyName}-msa-list`
+        : null, () => fetchMSAList({
+        config: selectedDataset.adapter,
+        pluginManager,
+        assemblyName,
+    }));
     const msaIds = useMemo(() => msaList && new Set(msaList), [msaList]);
     const transcriptSelection = useTranscriptSelection({
         feature,
@@ -49,9 +56,10 @@ const PreLoadedMSA = observer(function ({ model, feature, handleClose, preferred
         ? findDatasetId(selectedTranscript, feature, msaIds)
         : undefined;
     const { data: msaData, isLoading: msaDataLoading, error: msaDataFetchError, } = useFetch(msaId && selectedDataset
-        ? `${selectedDataset.datasetId}-${msaId}-msa`
+        ? `${selectedDataset.datasetId}-${assemblyName}-${msaId}-msa`
         : null, () => fetchMSA({
         msaId: msaId,
+        assemblyName,
         config: selectedDataset.adapter,
         pluginManager,
     }));
@@ -61,12 +69,12 @@ const PreLoadedMSA = observer(function ({ model, feature, handleClose, preferred
     // checked, and a name the alignment does not carry fails silently: the view
     // opens, renders, and never navigates. The row is found by sequence instead,
     // the same way the Manual tab finds it.
-    const queryRow = useQueryRowName(msaText, proteinSequence);
+    const queryRow = useQueryRowName(msaText, proteinSequence, msaData?.queryRowName);
     // The name this panel used to launch with unconditionally. A dataset built to
     // that convention does carry the row, so it is worth falling back to when the
     // residues do not match closely enough to find it -- but only when the
     // alignment really has it, which is the check the old code never made.
-    const querySeqName = resolveQueryRowName(queryRow, `${msaId ?? ''}_${assemblyNames[0] ?? ''}`);
+    const querySeqName = resolveQueryRowName(queryRow, `${msaId ?? ''}_${assemblyName ?? ''}`);
     const e = msaListFetchError ??
         msaDataFetchError ??
         transcriptSelection.error ??

package/dist/LaunchMsaView/components/PreLoadedMSA/fetchMSAData.d.ts

@@ -3,13 +3,17 @@ import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
 export interface DatasetMsa {
     msa: string;
     tree?: string;
+    /** the row the dataset names as the protein's own, preferred over a row that matches it equally */
+    queryRowName?: string;
 }
-export declare function fetchMSAList({ config, pluginManager, }: {
+export declare function fetchMSAList({ config, pluginManager, assemblyName, }: {
     config: AnyConfigurationModel;
     pluginManager: PluginManager;
+    assemblyName?: string;
 }): Promise<string[]>;
-export declare function fetchMSA({ config, pluginManager, msaId, }: {
+export declare function fetchMSA({ config, pluginManager, msaId, assemblyName, }: {
     config: AnyConfigurationModel;
     pluginManager: PluginManager;
     msaId: string;
+    assemblyName?: string;
 }): Promise<DatasetMsa>;

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

@@ -3,11 +3,11 @@ async function getMsaAdapter(pluginManager, config) {
     const result = await getAdapter(pluginManager, 'msa', config);
     return result.dataAdapter;
 }
-export async function fetchMSAList({ config, pluginManager, }) {
+export async function fetchMSAList({ config, pluginManager, assemblyName, }) {
     const adapter = await getMsaAdapter(pluginManager, config);
-    return adapter.getMSAList();
+    return adapter.getMSAList(assemblyName);
 }
-export async function fetchMSA({ config, pluginManager, msaId, }) {
+export async function fetchMSA({ config, pluginManager, msaId, assemblyName, }) {
     const adapter = await getMsaAdapter(pluginManager, config);
-    return adapter.getMSA(msaId);
+    return adapter.getMSA(msaId, assemblyName);
 }

package/dist/LaunchMsaView/components/pickSelectedId.test.d.ts

@@ -0,0 +1 @@
+export {};

package/dist/LaunchMsaView/components/pickSelectedId.test.js

@@ -0,0 +1,17 @@
+import { SimpleFeature } from '@jbrowse/core/util';
+import { expect, test } from 'vitest';
+import { pickSelectedId } from './useTranscriptSelection';
+const transcript = (id) => new SimpleFeature({ uniqueId: id, refName: '2L', start: 0, end: 10 });
+const options = ['t1', 't2', 't3'].map(transcript);
+test('with no hasData the selection always stands', () => {
+    expect(pickSelectedId('t2', options, undefined)).toBe('t2');
+});
+test('a selection with data stands', () => {
+    expect(pickSelectedId('t2', options, () => true)).toBe('t2');
+});
+test('a selection without data moves to the first option that has some', () => {
+    expect(pickSelectedId('t1', options, t => t.id() !== 't1')).toBe('t2');
+});
+test('with no option holding data the selection stands', () => {
+    expect(pickSelectedId('t3', options, () => false)).toBe('t3');
+});

package/dist/LaunchMsaView/components/useTranscriptSelection.d.ts

@@ -1,5 +1,6 @@
 import type { SequenceStatus } from './SequenceStatus';
 import type { Feature } from '@jbrowse/core/util';
+export declare function pickSelectedId(currentId: string, options: Feature[], hasData: ((transcript: Feature) => boolean) | undefined): string;
 export declare function useTranscriptSelection({ feature, view, hasData, preferredTranscriptId, }: {
     feature: Feature;
     view: {

package/dist/LaunchMsaView/components/useTranscriptSelection.js

@@ -4,7 +4,7 @@ import { useFeatureSequence } from './useFeatureSequence';
 // Keep the current selection if it has data, otherwise fall back to the first
 // option that does (or the current id if none do). With no hasData constraint
 // the current selection always stands.
-function pickSelectedId(currentId, options, hasData) {
+export function pickSelectedId(currentId, options, hasData) {
     if (!hasData) {
         return currentId;
     }

package/dist/LaunchMsaView/detectQueryRow.d.ts

@@ -44,4 +44,4 @@ export interface MsaQueryRow {
  * wanted on every keystroke in the paste box, and asking separately parsed a
  * few-hundred-row alignment twice per character.
  */
-export declare function findQueryRow(msaText: string, proteinSequence: string): MsaQueryRow;
+export declare function findQueryRow(msaText: string, proteinSequence: string, preferredName?: string): MsaQueryRow;

package/dist/LaunchMsaView/detectQueryRow.js

@@ -41,7 +41,7 @@ const PARTIAL_COVERAGE_FLOOR = 0.5;
  * wanted on every keystroke in the paste box, and asking separately parsed a
  * few-hundred-row alignment twice per character.
  */
-export function findQueryRow(msaText, proteinSequence) {
+export function findQueryRow(msaText, proteinSequence, preferredName) {
     if (!msaText.trim()) {
         return { names: [] };
     }
@@ -56,42 +56,54 @@ export function findQueryRow(msaText, proteinSequence) {
     }
     const names = parsed.getNames();
     const query = normalize(proteinSequence);
-    return { names, match: query ? bestMatch(parsed, names, query) : undefined };
+    return {
+        names,
+        match: query ? bestMatch(parsed, names, query, preferredName) : undefined,
+    };
 }
-function bestMatch(parsed, names, query) {
-    const candidates = [];
-    for (const name of names) {
-        const row = normalize(getUngappedSequence(parsed.getRow(name)));
-        if (!row) {
-            continue;
-        }
-        if (row === query) {
-            // nothing beats an exact match, and a second one would be a duplicate row
-            return { name, quality: 'exact', identity: 1, offset: 0 };
-        }
+function scoreRow(parsed, name, query) {
+    const row = normalize(getUngappedSequence(parsed.getRow(name)));
+    if (!row) {
+        return undefined;
+    }
+    else if (row === query) {
+        return { name, quality: 'exact', identity: 1, offset: 0 };
+    }
+    else {
         // BLAST reports the aligned region, so the row is often the query trimmed
         // at one or both ends rather than the whole protein
         const contained = query.indexOf(row);
         const containing = row.indexOf(query);
         if (contained !== -1 || containing !== -1) {
             const coverage = Math.min(row.length, query.length) / Math.max(row.length, query.length);
-            if (coverage >= PARTIAL_COVERAGE_FLOOR) {
-                candidates.push({
+            return coverage >= PARTIAL_COVERAGE_FLOOR
+                ? {
                     name,
                     quality: 'partial',
                     identity: coverage,
                     offset: contained === -1 ? -containing : contained,
-                });
-            }
-            continue;
+                }
+                : undefined;
         }
-        const identity = identityOverOverlap(row, query);
-        if (identity >= SIMILARITY_FLOOR) {
-            candidates.push({ name, quality: 'similar', identity, offset: 0 });
+        else {
+            const identity = identityOverOverlap(row, query);
+            return identity >= SIMILARITY_FLOOR
+                ? { name, quality: 'similar', identity, offset: 0 }
+                : undefined;
         }
     }
-    // an exact match returns above, so only these two can be here
-    const order = ['partial', 'similar'];
-    return candidates.sort((a, b) => order.indexOf(a.quality) - order.indexOf(b.quality) ||
-        b.identity - a.identity)[0];
+}
+const qualityOrder = ['exact', 'partial', 'similar'];
+/**
+ * The row matching the protein best. A paralog with an identical protein
+ * matches exactly as well as the query does, so a row the dataset itself names
+ * as the protein's own wins any tie.
+ */
+function bestMatch(parsed, names, query, preferredName) {
+    return names
+        .map(name => scoreRow(parsed, name, query))
+        .filter(match => match !== undefined)
+        .sort((a, b) => qualityOrder.indexOf(a.quality) - qualityOrder.indexOf(b.quality) ||
+        b.identity - a.identity ||
+        Number(b.name === preferredName) - Number(a.name === preferredName))[0];
 }

package/dist/LaunchMsaView/detectQueryRow.test.js

@@ -93,3 +93,12 @@ describe('findQueryRow row names', () => {
         expect(findQueryRow('', protein).names).toEqual([]);
     });
 });
+test("an identical paralog loses the tie to the row the dataset names as the protein's own", () => {
+    const msa = '>sp_H4copy\nMSGRGKGG\n>sp_His4r\nMSGRGKGG\n>sp_other\nMSGRGKAA\n';
+    expect(findQueryRow(msa, 'MSGRGKGG').match?.name).toBe('sp_H4copy');
+    expect(findQueryRow(msa, 'MSGRGKGG', 'sp_His4r').match?.name).toBe('sp_His4r');
+});
+test('a named row that matches worse than another does not win', () => {
+    const msa = '>sp_exact\nMSGRGKGG\n>sp_named\nMSGRGKAA\n';
+    expect(findQueryRow(msa, 'MSGRGKGG', 'sp_named').match?.name).toBe('sp_exact');
+});

package/dist/LaunchMsaView/useQueryRowName.d.ts

@@ -18,7 +18,7 @@ export declare function resolveQueryRowName(queryRow: {
     querySeqName: string;
     names: string[];
 }, fallback: string): string;
-export declare function useQueryRowName(msaText: string, proteinSequence: string): {
+export declare function useQueryRowName(msaText: string, proteinSequence: string, preferredName?: string): {
     detected: import("./detectQueryRow").QueryRowMatch | undefined;
     names: string[];
     querySeqName: string;

package/dist/LaunchMsaView/useQueryRowName.js

@@ -19,11 +19,11 @@ import { findQueryRow } from './detectQueryRow';
 export function resolveQueryRowName(queryRow, fallback) {
     return (queryRow.querySeqName || (queryRow.names.includes(fallback) ? fallback : ''));
 }
-export function useQueryRowName(msaText, proteinSequence) {
+export function useQueryRowName(msaText, proteinSequence, preferredName) {
     const [override, setOverride] = useState();
     // parsing runs on every keystroke in the paste box otherwise, and an
     // alignment of a few hundred rows is not free
-    const { names, match } = useMemo(() => findQueryRow(msaText, proteinSequence), [msaText, proteinSequence]);
+    const { names, match } = useMemo(() => findQueryRow(msaText, proteinSequence, preferredName), [msaText, proteinSequence, preferredName]);
     // a row picked from one alignment says nothing about the next one pasted
     const picked = override !== undefined && (names.length === 0 || names.includes(override))
         ? override

package/dist/MsaViewPanel/model.d.ts

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