react-msaview 8.3.0 → 8.4.1

package/dist/components/tracks/useTrackHover.js

@@ -1,8 +1,10 @@
+import { dragSelection } from '../selectionDrag.js';
 import { useHoverAnchor } from '../useHoverAnchor.js';
 /**
  * Translates pointer events over a track's row into the hovered column and a
  * tooltip anchor. The track shares the alignment's columns, so hovering it sets
- * the model's mouse column too and the alignment's hover band follows along.
+ * the model's mouse column too and the alignment's hover band follows along. A
+ * drag along the row selects the columns it covers across every row.
  *
  * `tooltip` off skips the anchor, so a track whose tooltip is turned off still
  * drives the hover band without re-rendering on every mouse move.
@@ -11,20 +13,38 @@ export function useTrackHover({ model, tooltip, }) {
     const { anchor, hoverAt, clearAnchor } = useHoverAnchor();
     // the blocks are laid out in column space and scrolled by a transform on
     // their container, so the pointer's column comes off the untransformed row
+    function colAt(clientX, left) {
+        return Math.floor((clientX - left - model.scrollX) / model.colWidth);
+    }
     function onMouseMove(event, el) {
-        const { colWidth, scrollX, numColumns } = model;
-        const { left } = el.getBoundingClientRect();
-        const col = Math.floor((event.clientX - left - scrollX) / colWidth);
-        const hit = col >= 0 && col < numColumns;
+        const col = colAt(event.clientX, el.getBoundingClientRect().left);
+        const hit = col >= 0 && col < model.numColumns;
         model.setMousePos(hit ? col : undefined, undefined);
         if (tooltip) {
             hoverAt(event, hit ? col : undefined);
         }
     }
+    // a press on a track's canvas, which leaves out the resize divider under it.
+    // The row takes the focus, so Escape reaches onMsaKey from there too
+    function onMouseDown(event, el) {
+        if (event.button === 0 && event.target instanceof HTMLCanvasElement) {
+            event.preventDefault();
+            el.focus({ preventScroll: true });
+            const { left } = el.getBoundingClientRect();
+            dragSelection(model, event, ({ clientX }) => ({
+                col: colAt(clientX, left),
+            }));
+        }
+    }
     function onMouseLeave() {
         clearAnchor();
         model.setMousePos(undefined, undefined);
     }
-    return { anchor: tooltip ? anchor : undefined, onMouseMove, onMouseLeave };
+    return {
+        anchor: tooltip ? anchor : undefined,
+        onMouseMove,
+        onMouseDown,
+        onMouseLeave,
+    };
 }
 //# sourceMappingURL=useTrackHover.js.map

package/dist/components/tracks/useTrackHover.js.map

@@ -1 +1 @@
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package/dist/components/tree/dialogs/TreeNodeInfoDialog.js

@@ -1,9 +1,8 @@
 import React from 'react';
-import Attributes from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/Attributes';
-import BaseCard from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard';
 import { Dialog } from '@jbrowse/core/ui';
-import { DialogContent } from '@mui/material';
+import { DialogContent, Typography } from '@mui/material';
 import { observer } from 'mobx-react';
+import MetadataTable from '../../MetadataTable.js';
 import SequenceTextArea from '../../SequenceTextArea.js';
 const TreeNodeInfoDialog = observer(function ({ info, model, nodeName, onClose, }) {
     const { rows } = model;
@@ -13,11 +12,13 @@ const TreeNodeInfoDialog = observer(function ({ info, model, nodeName, onClose,
             onClose();
         }, open: true, title: "Tree node info", maxWidth: "xl" },
         React.createElement(DialogContent, null,
-            React.createElement(BaseCard, { title: "Attributes" },
-                React.createElement(Attributes, { attributes: { nodeName, ...info } })),
-            React.createElement(BaseCard, { title: "Sequence" }, res ? (React.createElement(SequenceTextArea, { str: [res] })) : (React.createElement("div", null, "Sequence not found"))),
-            metadata ? (React.createElement(BaseCard, { title: "Extra metadata" },
-                React.createElement(Attributes, { attributes: metadata }))) : null)));
+            React.createElement(Typography, { variant: "h6" }, "Attributes"),
+            React.createElement(MetadataTable, { record: { nodeName, ...info } }),
+            React.createElement(Typography, { variant: "h6" }, "Sequence"),
+            res ? (React.createElement(SequenceTextArea, { str: [res] })) : (React.createElement(Typography, null, "Sequence not found")),
+            metadata ? (React.createElement(React.Fragment, null,
+                React.createElement(Typography, { variant: "h6" }, "Extra metadata"),
+                React.createElement(MetadataTable, { record: metadata }))) : null)));
 });
 export default TreeNodeInfoDialog;
 //# sourceMappingURL=TreeNodeInfoDialog.js.map

package/dist/components/tree/dialogs/TreeNodeInfoDialog.js.map

@@ -1 +1 @@
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package/dist/constants.d.ts

@@ -45,7 +45,7 @@ export declare const maxNeighborJoiningRows = 500;
 export declare const rowTintAlpha = 0.25;
 export declare const cladeHighlightColor = "#fff3c4";
 export declare const cladeHighlightAlpha = 0.6;
-export declare const maxInlineSnapshotBytes = 15000;
+export declare const maxInlineSnapshotBytes = 50000;
 export declare const rowPanelHeaderHeight = 56;
 export declare const treeScaleBarHeight = 22;
 export declare const defaultFeaturePanelWidth = 200;

package/dist/constants.js

@@ -90,12 +90,12 @@ export const rowTintAlpha = 0.25;
 // and the opacity a producer's own color takes when it carries none.
 export const cladeHighlightColor = '#fff3c4';
 export const cladeHighlightAlpha = 0.6;
-// The largest inline document the snapshot carries. A larger pasted or
-// locally-opened file stays in the live model and out of the snapshot, and
-// `unshareableData` warns using the same number. The demo app gzips the
-// snapshot into `?data=`, where 15 kB of the hosted protein alignments encodes
-// to 6,300-7,600 characters, under the 8,192 gmod.org accepts.
-export const maxInlineSnapshotBytes = 15_000;
+// The largest inline document a snapshot carries by default, which keeps a
+// jbrowse session small. A larger pasted or locally-opened file stays in the
+// live model and out of the snapshot, and `unshareableData` warns using the
+// same number. `MSAModelF({ maxInlineSnapshotBytes })` sets another; the demo
+// app's links hold far more.
+export const maxInlineSnapshotBytes = 50_000;
 // Height of the band the `rowPanels` headers draw in, above the strips in the
 // top area beside the tree ruler and the minimap. A panel wider than the band
 // is tall writes its header across, where it has more room.

package/dist/constants.js.map

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package/dist/element.d.ts

@@ -1,9 +1,13 @@
 /**
  * Registers a custom element that renders MSAViewer, for pages with no React.
  * Attributes: msa-url, tree-url, gff-url, color-scheme, height, hide-header,
- * theme, tree-area-width and reference-row. Properties: msa, tree and gff text, highlights,
- * columnTracks and residueMappings. Events: cell-hover, cell-click and
- * viewport-change, each with the MSAViewer callback's value as detail.
+ * theme, tree-area-width and reference-row. Properties: msa, tree and gff text,
+ * features, colorScheme, highlights, columnTracks, residueMappings and
+ * selection. The
+ * colorScheme property takes a `{map}` the color-scheme attribute cannot hold,
+ * and wins over the attribute while set. Events: cell-hover, cell-click,
+ * viewport-change and selection-change, each with the MSAViewer callback's
+ * value as detail.
  *
  * Inside a <nightingale-manager>, the element registers with it and speaks its
  * protocol: it follows the display-start, display-end and highlight attributes

package/dist/element.js

@@ -48,9 +48,13 @@ function residueRange(model, row, viewport) {
 /**
  * Registers a custom element that renders MSAViewer, for pages with no React.
  * Attributes: msa-url, tree-url, gff-url, color-scheme, height, hide-header,
- * theme, tree-area-width and reference-row. Properties: msa, tree and gff text, highlights,
- * columnTracks and residueMappings. Events: cell-hover, cell-click and
- * viewport-change, each with the MSAViewer callback's value as detail.
+ * theme, tree-area-width and reference-row. Properties: msa, tree and gff text,
+ * features, colorScheme, highlights, columnTracks, residueMappings and
+ * selection. The
+ * colorScheme property takes a `{map}` the color-scheme attribute cannot hold,
+ * and wins over the attribute while set. Events: cell-hover, cell-click,
+ * viewport-change and selection-change, each with the MSAViewer callback's
+ * value as detail.
  *
  * Inside a <nightingale-manager>, the element registers with it and speaks its
  * protocol: it follows the display-start, display-end and highlight attributes
@@ -89,6 +93,18 @@ export function defineMsaElement(tagName = 'jbrowse-msa') {
         set gff(value) {
             this.#setData({ gff: value });
         }
+        get features() {
+            return this.#data.features;
+        }
+        set features(value) {
+            this.#setData({ features: value });
+        }
+        get colorScheme() {
+            return this.#data.colorScheme;
+        }
+        set colorScheme(value) {
+            this.#setData({ colorScheme: value });
+        }
         get highlights() {
             return this.#data.highlights;
         }
@@ -107,6 +123,13 @@ export function defineMsaElement(tagName = 'jbrowse-msa') {
         set residueMappings(value) {
             this.#setData({ residueMappings: value });
         }
+        // the viewer's selection, which the reader's drags change
+        get selection() {
+            return this.#model ? this.#model.selection : this.#data.selection;
+        }
+        set selection(value) {
+            this.#setData({ selection: value });
+        }
         get #referenceRow() {
             return this.getAttribute('reference-row') ?? undefined;
         }
@@ -121,7 +144,9 @@ export function defineMsaElement(tagName = 'jbrowse-msa') {
                 msaFilehandle: location(this.getAttribute('msa-url')),
                 treeFilehandle: location(this.getAttribute('tree-url')),
                 gffFilehandle: location(this.getAttribute('gff-url')),
-                colorScheme: this.getAttribute('color-scheme') ?? undefined,
+                colorScheme: this.#data.colorScheme ??
+                    this.getAttribute('color-scheme') ??
+                    undefined,
                 height: numberAttribute(this.getAttribute('height')),
                 treeAreaWidth: numberAttribute(this.getAttribute('tree-area-width')),
                 hideHeader: this.hasAttribute('hide-header'),
@@ -137,6 +162,9 @@ export function defineMsaElement(tagName = 'jbrowse-msa') {
                     this.#emit('viewport-change', viewport);
                     this.#reportRange(viewport);
                 },
+                onSelectionChange: selection => {
+                    this.#emit('selection-change', selection);
+                },
                 onModel: model => {
                     this.#model = model;
                     this.#followRange();

package/dist/element.js.map

@@ -1 +1 @@
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package/dist/featuresLayer.d.ts

@@ -0,0 +1,8 @@
+import type { Annotation, Feature } from './types.ts';
+/**
+ * The `features` layer as the annotations a GFF would parse to. Every field
+ * but the placement is also an attribute, as a string like a GFF value, so an
+ * encoding reads `type` or a host's own field the way it reads a GFF column 9
+ * key.
+ */
+export declare function featuresToAnnotations(features: Feature[]): Annotation[];

package/dist/featuresLayer.js

@@ -0,0 +1,42 @@
+const placement = new Set(['row', 'start', 'end']);
+// The colors and labels are maps keyed by annotation, and a getter read
+// outside a reaction recomputes on every read. Caching on the frozen feature
+// gives it one annotation however often the layer converts.
+const converted = new WeakMap();
+/**
+ * The `features` layer as the annotations a GFF would parse to. Every field
+ * but the placement is also an attribute, as a string like a GFF value, so an
+ * encoding reads `type` or a host's own field the way it reads a GFF column 9
+ * key.
+ */
+export function featuresToAnnotations(features) {
+    return features.map(feature => {
+        const cached = converted.get(feature);
+        if (cached) {
+            return cached;
+        }
+        const annotation = featureAnnotation(feature);
+        converted.set(feature, annotation);
+        return annotation;
+    });
+}
+function featureAnnotation(feature) {
+    const { row, start, end, name, description, type, strand, color } = feature;
+    const accession = name ?? `${row}:${start}-${end}`;
+    const attributes = Object.fromEntries(Object.entries(feature)
+        .filter(([key, value]) => !placement.has(key) && value !== undefined)
+        .map(([key, value]) => [key, String(value)]));
+    return {
+        id: row,
+        accession,
+        name: name ?? accession,
+        description: description ?? name ?? accession,
+        featureType: type,
+        start,
+        end,
+        strand: strand === '+' ? 1 : strand === '-' ? -1 : undefined,
+        color,
+        attributes,
+    };
+}
+//# sourceMappingURL=featuresLayer.js.map

package/dist/featuresLayer.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"featuresLayer.js","sourceRoot":"","sources":["../src/featuresLayer.ts"],"names":[],"mappings":"AAEA,MAAM,SAAS,GAAG,IAAI,GAAG,CAAC,CAAC,KAAK,EAAE,OAAO,EAAE,KAAK,CAAC,CAAC,CAAA;AAElD,wEAAwE;AACxE,6EAA6E;AAC7E,4DAA4D;AAC5D,MAAM,SAAS,GAAG,IAAI,OAAO,EAAuB,CAAA;AAEpD;;;;;GAKG;AACH,MAAM,UAAU,qBAAqB,CAAC,QAAmB;IACvD,OAAO,QAAQ,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE;QAC5B,MAAM,MAAM,GAAG,SAAS,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;QACrC,IAAI,MAAM,EAAE,CAAC;YACX,OAAO,MAAM,CAAA;QACf,CAAC;QACD,MAAM,UAAU,GAAG,iBAAiB,CAAC,OAAO,CAAC,CAAA;QAC7C,SAAS,CAAC,GAAG,CAAC,OAAO,EAAE,UAAU,CAAC,CAAA;QAClC,OAAO,UAAU,CAAA;IACnB,CAAC,CAAC,CAAA;AACJ,CAAC;AAED,SAAS,iBAAiB,CAAC,OAAgB;IACzC,MAAM,EAAE,GAAG,EAAE,KAAK,EAAE,GAAG,EAAE,IAAI,EAAE,WAAW,EAAE,IAAI,EAAE,MAAM,EAAE,KAAK,EAAE,GAAG,OAAO,CAAA;IAC3E,MAAM,SAAS,GAAG,IAAI,IAAI,GAAG,GAAG,IAAI,KAAK,IAAI,GAAG,EAAE,CAAA;IAClD,MAAM,UAAU,GAAG,MAAM,CAAC,WAAW,CACnC,MAAM,CAAC,OAAO,CAAC,OAAO,CAAC;SACpB,MAAM,CAAC,CAAC,CAAC,GAAG,EAAE,KAAK,CAAC,EAAE,EAAE,CAAC,CAAC,SAAS,CAAC,GAAG,CAAC,GAAG,CAAC,IAAI,KAAK,KAAK,SAAS,CAAC;SACpE,GAAG,CAAC,CAAC,CAAC,GAAG,EAAE,KAAK,CAAC,EAAE,EAAE,CAAC,CAAC,GAAG,EAAE,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,CAC/C,CAAA;IACD,OAAO;QACL,EAAE,EAAE,GAAG;QACP,SAAS;QACT,IAAI,EAAE,IAAI,IAAI,SAAS;QACvB,WAAW,EAAE,WAAW,IAAI,IAAI,IAAI,SAAS;QAC7C,WAAW,EAAE,IAAI;QACjB,KAAK;QACL,GAAG;QACH,MAAM,EAAE,MAAM,KAAK,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,MAAM,KAAK,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS;QAC5D,KAAK;QACL,UAAU;KACX,CAAA;AACH,CAAC"}

package/dist/index.d.ts

@@ -19,4 +19,4 @@ export type { InterProScanResults } from 'msa-parsers';
 export type { ColumnCounts } from './columnCounts.ts';
 export type { ColumnStats } from './columnStats.ts';
 export type { ResolvedScale, ScaleSpec } from './scales.ts';
-export type { Accession, Annotation, Arc, ArcSpec, ArcTrackModel, BasicTrack, BasicTrackModel, Cell, Clade, CladeMark, ColumnTrackSpec, DomainBand, Encoding, EncodingChannel, Highlight, Legend, LegendEntry, Node, MappedStructure, NodeWithIds, NodeWithIdsAndLength, Region, ResidueEncoding, ResidueMapping, ResidueMappingProblem, ResidueSegment, ResolvedClade, ResolvedEncoding, ResolvedHighlight, ResolvedRowPanel, RowPanelSpec, RowResidue, StructureResidue, TextTrackModel, TidyDomainAnnotation, TrackKind, TreeOrder, TreeRoot, UnshareableData, Viewport, } from './types.ts';
+export type { Accession, Annotation, Arc, ArcSpec, ArcTrackModel, BasicTrack, BasicTrackModel, Cell, Clade, CladeMark, ColorScheme, ColumnTrackSpec, DomainBand, Encoding, EncodingChannel, Feature, Highlight, Legend, LegendEntry, MsaSelection, Node, MappedStructure, NodeWithIds, NodeWithIdsAndLength, Region, ResidueEncoding, ResidueMapping, ResidueMappingProblem, ResidueSegment, ResolvedClade, ResolvedEncoding, ResolvedHighlight, ResolvedRowPanel, ResolvedSelection, RowDataInput, RowPanelSpec, RowResidue, StructureResidue, TextTrackModel, TidyDomainAnnotation, TrackKind, TreeOrder, TreeRoot, UnshareableData, Viewport, } from './types.ts';

package/dist/model/DataModel.d.ts

@@ -5,7 +5,7 @@
  * data will not be persisted in saved session snapshots, it will be fetched
  * from msaFilehandle at startup
  */
-export declare function DataModelF(): import("@jbrowse/mobx-state-tree").IModelType<{
+export declare function DataModelF(maxInlineBytes?: number): import("@jbrowse/mobx-state-tree").IModelType<{
     /**
      * #property
      */

package/dist/model/DataModel.js

@@ -7,7 +7,7 @@ import { maxInlineSnapshotBytes } from '../constants.js';
  * data will not be persisted in saved session snapshots, it will be fetched
  * from msaFilehandle at startup
  */
-export function DataModelF() {
+export function DataModelF(maxInlineBytes = maxInlineSnapshotBytes) {
     return types
         .model({
         /**
@@ -54,11 +54,11 @@ export function DataModelF() {
         },
     }))
         .postProcessSnapshot(snap => 
-    // drops any field over maxInlineSnapshotBytes; the parent model's
+    // drops any field over maxInlineBytes; the parent model's
     // `unshareableData` reports what was dropped
     Object.fromEntries(Object.entries(snap).map(([key, text]) => [
         key,
-        text && text.length > maxInlineSnapshotBytes ? undefined : text,
+        text && text.length > maxInlineBytes ? undefined : text,
     ])));
 }
 //# sourceMappingURL=DataModel.js.map

package/dist/model/DataModel.js.map

@@ -1 +1 @@
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+{"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

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