react-msaview 8.3.0 → 8.4.0

package/dist/model/DataModel.js.map

@@ -1 +1 @@
-{"version":3,"file":"DataModel.js","sourceRoot":"","sources":["../../src/model/DataModel.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,0BAA0B,CAAA;AAEhD,OAAO,EAAE,sBAAsB,EAAE,MAAM,iBAAiB,CAAA;AAExD;;;;;;GAMG;AACH,MAAM,UAAU,UAAU;IACxB,OAAO,KAAK;SACT,KAAK,CAAC;QACL;;WAEG;QACH,IAAI,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;QAC/B;;WAEG;QACH,GAAG,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;QAC9B;;WAEG;QACH,YAAY,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;QACvC;;WAEG;QACH,GAAG,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;KAC/B,CAAC;SACD,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB;;WAEG;QACH,OAAO,CAAC,IAAa;YACnB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAClB,CAAC;QACD;;WAEG;QACH,MAAM,CAAC,GAAY;YACjB,IAAI,CAAC,GAAG,GAAG,GAAG,CAAA;QAChB,CAAC;QACD;;WAEG;QACH,eAAe,CAAC,YAAqB;YACnC,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA;QAClC,CAAC;QACD;;WAEG;QACH,MAAM,CAAC,GAAY;YACjB,IAAI,CAAC,GAAG,GAAG,GAAG,CAAA;QAChB,CAAC;KACF,CAAC,CAAC;SACF,mBAAmB,CAAC,IAAI,CAAC,EAAE;IAC1B,kEAAkE;IAClE,6CAA6C;IAC7C,MAAM,CAAC,WAAW,CAChB,MAAM,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,EAAE,IAAI,CAAC,EAAE,EAAE,CAAC;QACxC,GAAG;QACH,IAAI,IAAI,IAAI,CAAC,MAAM,GAAG,sBAAsB,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI;KAChE,CAAC,CACH,CACF,CAAA;AACL,CAAC"}
+{"version":3,"file":"DataModel.js","sourceRoot":"","sources":["../../src/model/DataModel.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,0BAA0B,CAAA;AAEhD,OAAO,EAAE,sBAAsB,EAAE,MAAM,iBAAiB,CAAA;AAExD;;;;;;GAMG;AACH,MAAM,UAAU,UAAU,CAAC,cAAc,GAAG,sBAAsB;IAChE,OAAO,KAAK;SACT,KAAK,CAAC;QACL;;WAEG;QACH,IAAI,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;QAC/B;;WAEG;QACH,GAAG,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;QAC9B;;WAEG;QACH,YAAY,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;QACvC;;WAEG;QACH,GAAG,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;KAC/B,CAAC;SACD,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB;;WAEG;QACH,OAAO,CAAC,IAAa;YACnB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAClB,CAAC;QACD;;WAEG;QACH,MAAM,CAAC,GAAY;YACjB,IAAI,CAAC,GAAG,GAAG,GAAG,CAAA;QAChB,CAAC;QACD;;WAEG;QACH,eAAe,CAAC,YAAqB;YACnC,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA;QAClC,CAAC;QACD;;WAEG;QACH,MAAM,CAAC,GAAY;YACjB,IAAI,CAAC,GAAG,GAAG,GAAG,CAAA;QAChB,CAAC;KACF,CAAC,CAAC;SACF,mBAAmB,CAAC,IAAI,CAAC,EAAE;IAC1B,0DAA0D;IAC1D,6CAA6C;IAC7C,MAAM,CAAC,WAAW,CAChB,MAAM,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,EAAE,IAAI,CAAC,EAAE,EAAE,CAAC;QACxC,GAAG;QACH,IAAI,IAAI,IAAI,CAAC,MAAM,GAAG,cAAc,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI;KACxD,CAAC,CACH,CACF,CAAA;AACL,CAAC"}

package/dist/model/msaModel.d.ts

@@ -13,6 +13,12 @@ export declare function MSAModelF(): import("@jbrowse/mobx-state-tree").IModelTy
      * default color scheme name
      */
     colorSchemeName: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+    /**
+     * #property
+     * a color per residue letter, which replaces the `colorSchemeName` table
+     * while set. A letter the map leaves out takes no color
+     */
+    customColorScheme: import("@jbrowse/mobx-state-tree").IType<Record<string, string> | undefined, Record<string, string> | undefined, Record<string, string> | undefined>;
     /**
      * #property
      * show a tooltip with the hovered column's value for a track while
@@ -29,9 +35,16 @@ export declare function MSAModelF(): import("@jbrowse/mobx-state-tree").IModelTy
 }, {
     /**
      * #action
-     * set color scheme name
+     * pick a scheme from the built-in table, which clears
+     * `customColorScheme`
      */
     setColorSchemeName(name: string): void;
+    /**
+     * #action
+     * color residues from a map of letter to color, or pass undefined to
+     * return to `colorSchemeName`
+     */
+    setCustomColorScheme(map?: Record<string, string>): void;
     /**
      * #action
      */

package/dist/model/msaModel.js

@@ -18,6 +18,12 @@ export function MSAModelF() {
          * default color scheme name
          */
         colorSchemeName: stripDefault(types.string, defaultColorSchemeName),
+        /**
+         * #property
+         * a color per residue letter, which replaces the `colorSchemeName` table
+         * while set. A letter the map leaves out takes no color
+         */
+        customColorScheme: types.frozen(),
         /**
          * #property
          * show a tooltip with the hovered column's value for a track while
@@ -35,10 +41,20 @@ export function MSAModelF() {
         .actions(self => ({
         /**
          * #action
-         * set color scheme name
+         * pick a scheme from the built-in table, which clears
+         * `customColorScheme`
          */
         setColorSchemeName(name) {
             self.colorSchemeName = name;
+            self.customColorScheme = undefined;
+        },
+        /**
+         * #action
+         * color residues from a map of letter to color, or pass undefined to
+         * return to `colorSchemeName`
+         */
+        setCustomColorScheme(map) {
+            self.customColorScheme = map;
         },
         /**
          * #action

package/dist/model/msaModel.js.map

@@ -1 +1 @@
-{"version":3,"file":"msaModel.js","sourceRoot":"","sources":["../../src/model/msaModel.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,0BAA0B,CAAA;AAEhD,OAAO,EACL,cAAc,EACd,sBAAsB,EACtB,sBAAsB,GACvB,MAAM,iBAAiB,CAAA;AACxB,OAAO,EAAE,YAAY,EAAE,MAAM,oBAAoB,CAAA;AAIjD,MAAM,UAAU,GAAgB,CAAC,WAAW,EAAE,KAAK,EAAE,OAAO,EAAE,KAAK,EAAE,SAAS,CAAC,CAAA;AAE/E;;GAEG;AACH,MAAM,UAAU,SAAS;IACvB,OAAO,KAAK;SACT,KAAK,CAAC;QACL;;;WAGG;QACH,OAAO,EAAE,YAAY,CAAC,KAAK,CAAC,OAAO,EAAE,cAAc,CAAC;QAEpD;;;WAGG;QACH,eAAe,EAAE,YAAY,CAAC,KAAK,CAAC,MAAM,EAAE,sBAAsB,CAAC;QAEnE;;;;;WAKG;QACH,eAAe,EAAE,YAAY,CAAC,KAAK,CAAC,OAAO,EAAE,sBAAsB,CAAC;QAEpE;;;;WAIG;QACH,SAAS,EAAE,KAAK,CAAC,KAAK,CACpB,KAAK,CAAC,WAAW,CAAY,WAAW,EAAE,UAAU,CAAC,CACtD;KACF,CAAC;SACD,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB;;;WAGG;QACH,kBAAkB,CAAC,IAAY;YAC7B,IAAI,CAAC,eAAe,GAAG,IAAI,CAAA;QAC7B,CAAC;QAED;;WAEG;QACH,UAAU,CAAC,GAAY;YACrB,IAAI,CAAC,OAAO,GAAG,GAAG,CAAA;QACpB,CAAC;QAED;;WAEG;QACH,kBAAkB,CAAC,GAAY;YAC7B,IAAI,CAAC,eAAe,GAAG,GAAG,CAAA;QAC5B,CAAC;QAED;;;WAGG;QACH,YAAY,CAAC,GAAe;YAC1B,IAAI,CAAC,SAAS,GAAG,GAAG,CAAA;QACtB,CAAC;KACF,CAAC,CAAC,CAAA;AACP,CAAC"}
+{"version":3,"file":"msaModel.js","sourceRoot":"","sources":["../../src/model/msaModel.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,0BAA0B,CAAA;AAEhD,OAAO,EACL,cAAc,EACd,sBAAsB,EACtB,sBAAsB,GACvB,MAAM,iBAAiB,CAAA;AACxB,OAAO,EAAE,YAAY,EAAE,MAAM,oBAAoB,CAAA;AAIjD,MAAM,UAAU,GAAgB,CAAC,WAAW,EAAE,KAAK,EAAE,OAAO,EAAE,KAAK,EAAE,SAAS,CAAC,CAAA;AAE/E;;GAEG;AACH,MAAM,UAAU,SAAS;IACvB,OAAO,KAAK;SACT,KAAK,CAAC;QACL;;;WAGG;QACH,OAAO,EAAE,YAAY,CAAC,KAAK,CAAC,OAAO,EAAE,cAAc,CAAC;QAEpD;;;WAGG;QACH,eAAe,EAAE,YAAY,CAAC,KAAK,CAAC,MAAM,EAAE,sBAAsB,CAAC;QAEnE;;;;WAIG;QACH,iBAAiB,EAAE,KAAK,CAAC,MAAM,EAAsC;QAErE;;;;;WAKG;QACH,eAAe,EAAE,YAAY,CAAC,KAAK,CAAC,OAAO,EAAE,sBAAsB,CAAC;QAEpE;;;;WAIG;QACH,SAAS,EAAE,KAAK,CAAC,KAAK,CACpB,KAAK,CAAC,WAAW,CAAY,WAAW,EAAE,UAAU,CAAC,CACtD;KACF,CAAC;SACD,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB;;;;WAIG;QACH,kBAAkB,CAAC,IAAY;YAC7B,IAAI,CAAC,eAAe,GAAG,IAAI,CAAA;YAC3B,IAAI,CAAC,iBAAiB,GAAG,SAAS,CAAA;QACpC,CAAC;QAED;;;;WAIG;QACH,oBAAoB,CAAC,GAA4B;YAC/C,IAAI,CAAC,iBAAiB,GAAG,GAAG,CAAA;QAC9B,CAAC;QAED;;WAEG;QACH,UAAU,CAAC,GAAY;YACrB,IAAI,CAAC,OAAO,GAAG,GAAG,CAAA;QACpB,CAAC;QAED;;WAEG;QACH,kBAAkB,CAAC,GAAY;YAC7B,IAAI,CAAC,eAAe,GAAG,GAAG,CAAA;QAC5B,CAAC;QAED;;;WAGG;QACH,YAAY,CAAC,GAAe;YAC1B,IAAI,CAAC,SAAS,GAAG,GAAG,CAAA;QACtB,CAAC;KACF,CAAC,CAAC,CAAA;AACP,CAAC"}

package/dist/model.d.ts

@@ -2,7 +2,7 @@ import type { ColumnStats } from './columnStats.ts';
 import type { ScrollZoomAxis } from './constants.ts';
 import type { HierarchyNode } from './hierarchy.ts';
 import type { ExportSvgOptions } from './renderToSvg.tsx';
-import type { Annotation, Arc, BasicTrack, Cell, Clade, ResidueMappingProblem, ColumnTrackSpec, DomainBand, Encoding, Highlight, Legend, NodeWithIds, Region, ResidueMapping, ResolvedClade, ResolvedEncoding, ResolvedFeaturePanel, ResolvedHighlight, TreeOrder, TreeRoot, ResolvedRowPanel, ResolvedStripPanel, RowPanelSpec, RowResidue, StructureResidue, TrackKind, UnshareableData, Viewport } from './types.ts';
+import type { Annotation, Arc, BasicTrack, Cell, Clade, ResidueMappingProblem, ColumnTrackSpec, DomainBand, Encoding, Feature, Highlight, Legend, MsaSelection, NodeWithIds, Region, ResidueMapping, ResolvedClade, ResolvedEncoding, ResolvedFeaturePanel, ResolvedHighlight, ResolvedSelection, TreeOrder, TreeRoot, ResolvedRowPanel, ResolvedStripPanel, RowDataInput, RowPanelSpec, RowResidue, StructureResidue, TrackKind, UnshareableData, Viewport } from './types.ts';
 import type { FileLocation as FileLocationType } from '@jbrowse/core/util/types';
 import type { Instance } from '@jbrowse/mobx-state-tree';
 import type { InterProScanResults } from 'msa-parsers';
@@ -41,8 +41,15 @@ export declare const preservedOnReset: Set<string>;
  * const root = RootModel.create({})
  * root.view.setData({ msa: '>seq1\nACGT\n>seq2\nACGT' })
  * ```
+ *
+ * `maxInlineSnapshotBytes` is the largest pasted or local document, and the
+ * largest data track, the snapshot keeps; a larger one stays in the live model
+ * and `unshareableData` names it. The standalone app, whose links carry the
+ * snapshot in the URL fragment, raises it.
  */
-declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelType<Omit<Omit<Omit<{}, "autoTreeAreaWidth" | "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "treeAreaWidth" | "treeOrder" | "treeWidth"> & {
+declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
+    maxInlineSnapshotBytes?: number;
+}): import("@jbrowse/mobx-state-tree").IModelType<Omit<Omit<Omit<{}, "autoTreeAreaWidth" | "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "treeAreaWidth" | "treeOrder" | "treeWidth"> & {
     drawLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     labelsAlignRight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     treeAreaWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
@@ -55,12 +62,13 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
     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" | "colorSchemeName" | "customColorScheme" | "msaFormat" | "showColumnStats"> & {
     bgColor: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     colorSchemeName: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+    customColorScheme: import("@jbrowse/mobx-state-tree").IType<Record<string, string> | undefined, Record<string, string> | undefined, Record<string, string> | undefined>;
     showColumnStats: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     msaFormat: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<import("msa-parsers").MSAFormat>>;
-}, "allowedGappyness" | "clades" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "drawMsaLetters" | "encodings" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "id" | "msaFilehandle" | "region" | "relativeTo" | "residueMappings" | "rotated" | "rowHeight" | "rowPanels" | "scrollX" | "scrollY" | "scrollZoom" | "scrollZoomAxis" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "trackHeights" | "treeFilehandle" | "treeMetadataFilehandle" | "treeRoot" | "turnedOffFeatures" | "turnedOffTracks" | "type"> & {
+}, "allowedGappyness" | "clades" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "drawMsaLetters" | "encodings" | "features" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "id" | "msaFilehandle" | "region" | "relativeTo" | "residueMappings" | "rotated" | "rowHeight" | "rowPanels" | "scrollX" | "scrollY" | "scrollZoom" | "scrollZoomAxis" | "selection" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "trackHeights" | "treeFilehandle" | "treeMetadataFilehandle" | "treeRoot" | "turnedOffFeatures" | "turnedOffTracks" | "type"> & {
     /**
      * #property
      * id of view, randomly generated if not provided
@@ -633,6 +641,21 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * Persists in the snapshot and the URL.
      */
     highlights: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<Highlight, Highlight, Highlight>>, [undefined]>;
+    /**
+     * #property
+     * features on the rows as data, `{row, start, end, name, ...}` in
+     * residues of each row, drawn with the GFF's annotations. Persists in
+     * the snapshot and the URL.
+     */
+    features: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<Feature, Feature, Feature>>, [undefined]>;
+    /**
+     * #property
+     * the block the reader selected: `{start, end}` columns of the file,
+     * 1-based inclusive like a column highlight, and `rows` by name, every
+     * row where absent. Undefined until something is selected, so a view
+     * without one adds nothing to the shared URL.
+     */
+    selection: import("@jbrowse/mobx-state-tree").IType<MsaSelection | undefined, MsaSelection | undefined, MsaSelection | undefined>;
     /**
      * #property
      * where the view opens, in `highlights` coordinates: `{row, start,
@@ -690,6 +713,7 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
     setDrawLabels(arg: boolean): void;
 } & {
     setColorSchemeName(name: string): void;
+    setCustomColorScheme(map?: Record<string, string>): void;
     setBgColor(arg: boolean): void;
     setShowColumnStats(arg: boolean): void;
     setMSAFormat(arg?: import("msa-parsers").MSAFormat): void;
@@ -903,6 +927,20 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * #action
      */
     setHighlights(highlights: Highlight[]): void;
+    /**
+     * #action
+     */
+    setFeatures(features: Feature[]): void;
+    /**
+     * #action
+     * select a block, in `selection` coordinates. `start` and `end` may come
+     * in either order.
+     */
+    setSelection(selection?: MsaSelection): void;
+    /**
+     * #action
+     */
+    clearSelection(): void;
     /**
      * #action
      * replace the clades the viewer marks (see docs/layers.md)
@@ -1026,9 +1064,9 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * store the GFF text in the snapshot like the alignment and tree. The
      * parsed annotations are volatile and a blob filehandle is cleared once
      * read, so the text is the only persisted copy. An autorun parses it
-     * into annotations.
+     * into annotations, and clears the ones it drew when the text goes.
      */
-    setGFF(result: string): void;
+    setGFF(result?: string): void;
 } & {
     /**
      * #getter
@@ -1039,6 +1077,12 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * #getter
      */
     readonly realAllowedGappyness: number;
+    /**
+     * #getter
+     * the annotations the overlay, the legend and the encodings draw: the
+     * GFF's, then the `features` layer's
+     */
+    readonly allAnnotations: Annotation[];
     /**
      * #getter
      */
@@ -1065,6 +1109,13 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * #getter
      */
     readonly colorScheme: Record<string, string>;
+    /**
+     * #getter
+     * the scheme coloring each cell from its column's statistics, or
+     * undefined while the cells take a fixed color per letter, from the
+     * built-in table or from `customColorScheme`
+     */
+    readonly dynamicColorSchemeName: string | undefined;
     /**
      * #getter
      */
@@ -1095,9 +1146,9 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * from disk or pasted in becomes inline text, and DataModel drops an
      * inline document past `maxInlineSnapshotBytes`.
      *
-     * The header lists these, and the standalone app drops `?data=` from
+     * The header lists these, and the standalone app drops `#data=` from
      * the address bar while the list is non-empty or the encoded link would
-     * pass 8,000 characters, so a copied link never opens an empty viewer
+     * pass its `maxLinkLength`, so a copied link never opens an empty viewer
      * unannounced. A document fetched from a URL never appears here, since
      * the snapshot keeps its filehandle.
      *
@@ -1112,7 +1163,8 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * `data.treeMetadata`, the name that travels in existing links, so the
      * inline size limit and `treeMetadataFilehandle` cover it. labelWidthMap
      * reads it on every layout, so a malformed user-supplied file returns {}
-     * instead of throwing out of rendering.
+     * instead of throwing out of rendering, and every field is a string by
+     * the time a scale sorts it.
      */
     readonly rowData: Record<string, Record<string, string> | undefined>;
     /**
@@ -1890,7 +1942,7 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * replace the row table, which the model keeps as the JSON string
      * `data.treeMetadata` (see docs/layers.md)
      */
-    setRowData(rowData: Record<string, Record<string, string>>): void;
+    setRowData(rowData: RowDataInput): void;
     /**
      * #action
      * replace what the viewer's marks read from the row table
@@ -2075,6 +2127,39 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * is dropped. Row names that match no row are ignored.
      */
     readonly resolvedHighlights: ResolvedHighlight[];
+    /**
+     * #getter
+     * `selection` projected onto what is on screen, the way
+     * `resolvedHighlights` projects a column span and a row set. A
+     * selection whose columns are all hidden, or whose rows are all
+     * collapsed away or unknown, resolves to undefined.
+     */
+    readonly resolvedSelection: ResolvedSelection | undefined;
+    /**
+     * #getter
+     * the columns and rows the selection covers, for the header's readout.
+     * Columns count the file's columns from `start` to `end`, hidden ones
+     * included, as `selectionFasta` copies them.
+     */
+    readonly selectionSize: {
+        columns: number;
+        rows: number;
+    } | undefined;
+    /**
+     * #getter
+     * `selection`'s columns clamped to the file's
+     */
+    readonly selectionFileSpan: {
+        start: number;
+        end: number;
+    } | undefined;
+    /**
+     * #getter
+     * the selected block as FASTA: the selected rows on screen, top to
+     * bottom, each with its letters across the file's columns from `start`
+     * to `end`, gaps included
+     */
+    readonly selectionFasta: string;
     /**
      * #method
      * per-column summary statistics: consensus residue and its identity
@@ -2097,7 +2182,7 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
     /**
      * #getter
      * each encoding with its scale resolved against the values its field
-     * takes: a feature channel reads them across the features drawn, every
+     * takes: a feature channel reads them across every feature loaded, every
      * other channel across the row table. Resolved once per change of that
      * table or the encodings, never per row per frame.
      */
@@ -2209,6 +2294,26 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * its width, or for a span that resolves to no visible column.
      */
     zoomToRegion(region: Region): void;
+    /**
+     * #action
+     * zoom and scroll so the selected columns fill the alignment's width,
+     * and, where the selection names its rows, so those rows fill its height
+     */
+    zoomToSelection(): void;
+    /**
+     * #action
+     * select the block between two cells given as visible column and row
+     * indices, the coordinates a drag reports, clamped to the alignment. A
+     * cell with no `row` selects the columns across every row, and so does a
+     * block spanning every row on screen.
+     */
+    selectBlock(anchor: {
+        col: number;
+        row?: number;
+    }, head: {
+        col: number;
+        row?: number;
+    }): void;
     /**
      * #action
      */
@@ -2217,6 +2322,7 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
 }, import("@jbrowse/mobx-state-tree")._NotCustomized, {
     bgColor: boolean;
     colorSchemeName: string;
+    customColorScheme: Record<string, string> | undefined;
     showColumnStats: boolean;
     msaFormat: import("msa-parsers").MSAFormat | undefined;
     drawLabels: boolean;
@@ -2339,6 +2445,8 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
     relativeTo: string | undefined;
     highlightColumns: number[] | undefined;
     highlights: Highlight[];
+    features: Feature[];
+    selection: MsaSelection | undefined;
     region: Region | undefined;
     clades: Clade[];
     encodings: Encoding[];
@@ -2352,6 +2460,7 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
 } | {
     bgColor: boolean;
     colorSchemeName: string;
+    customColorScheme: Record<string, string> | undefined;
     showColumnStats: boolean;
     msaFormat: import("msa-parsers").MSAFormat | undefined;
     drawLabels: boolean;
@@ -2474,6 +2583,8 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
     relativeTo: string | undefined;
     highlightColumns: number[] | undefined;
     highlights: Highlight[];
+    features: Feature[];
+    selection: MsaSelection | undefined;
     region: Region | undefined;
     clades: Clade[];
     encodings: Encoding[];