react-msaview 9.4.0 → 9.6.0

package/dist/components/MSAViewer.d.ts

@@ -141,7 +141,7 @@ export interface MSAViewerProps {
  * of those props changes and keeps its model across every other change,
  * including a new annotation file. A `ref` holds the current model.
  */
-declare const MSAViewer: React.ForwardRefExoticComponent<MSAViewerProps & React.RefAttributes<import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<Omit<Omit<Omit<{}, "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "showTreeScaleBar" | "treeAreaWidth" | "treeOrder" | "treeWidth"> & {
+declare const MSAViewer: React.ForwardRefExoticComponent<MSAViewerProps & React.RefAttributes<import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<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>>;
@@ -152,7 +152,6 @@ declare const MSAViewer: React.ForwardRefExoticComponent<MSAViewerProps & React.
     drawNodeBubbles: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     drawNodeLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     showTreeOverview: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-    showTreeScaleBar: 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]>;
 }, "bgColor" | "colorSchemeName" | "customColorScheme" | "msaFormat" | "showColumnStats"> & {
     bgColor: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
@@ -548,7 +547,6 @@ declare const MSAViewer: React.ForwardRefExoticComponent<MSAViewerProps & React.
     setDrawNodeBubbles(arg: boolean): void;
     setDrawNodeLabels(arg: boolean): void;
     setShowTreeOverview(arg: boolean): void;
-    setShowTreeScaleBar(arg: boolean): void;
     setDrawLabels(arg: boolean): void;
 } & {
     setColorSchemeName(name: string): void;
@@ -969,7 +967,7 @@ declare const MSAViewer: React.ForwardRefExoticComponent<MSAViewerProps & React.
     }): void;
     fitHorizontally(maxColWidth?: any): void;
     afterCreate(): void;
-} & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<Omit<Omit<Omit<{}, "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "showTreeScaleBar" | "treeAreaWidth" | "treeOrder" | "treeWidth"> & {
+} & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<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>>;
@@ -980,7 +978,6 @@ declare const MSAViewer: React.ForwardRefExoticComponent<MSAViewerProps & React.
     drawNodeBubbles: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     drawNodeLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     showTreeOverview: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-    showTreeScaleBar: 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]>;
 }, "bgColor" | "colorSchemeName" | "customColorScheme" | "msaFormat" | "showColumnStats"> & {
     bgColor: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
@@ -1376,7 +1373,6 @@ declare const MSAViewer: React.ForwardRefExoticComponent<MSAViewerProps & React.
     setDrawNodeBubbles(arg: boolean): void;
     setDrawNodeLabels(arg: boolean): void;
     setShowTreeOverview(arg: boolean): void;
-    setShowTreeScaleBar(arg: boolean): void;
     setDrawLabels(arg: boolean): void;
 } & {
     setColorSchemeName(name: string): void;
@@ -1813,7 +1809,6 @@ declare const MSAViewer: React.ForwardRefExoticComponent<MSAViewerProps & React.
     drawNodeBubbles: boolean;
     drawNodeLabels: boolean;
     showTreeOverview: boolean;
-    showTreeScaleBar: boolean;
     overviewHeight: number;
     columnTracks: ColumnTrackSpec[];
     id: string;
@@ -1953,7 +1948,6 @@ declare const MSAViewer: React.ForwardRefExoticComponent<MSAViewerProps & React.
     drawNodeBubbles: boolean;
     drawNodeLabels: boolean;
     showTreeOverview: boolean;
-    showTreeScaleBar: boolean;
     overviewHeight: number;
     columnTracks?: undefined;
     id: string;

package/dist/components/header/menuBarItems.js

@@ -118,7 +118,7 @@ function outgroupLabel(outgroup) {
         : `Outgroup ${first} … ${rest.at(-1)}`;
 }
 export function treeSubMenu(model) {
-    const { drawTree, showBranchLen, labelsAlignRight, drawNodeLabels, drawLabels, treeAreaWidth, showTreeOverview, showTreeScaleBar, treeOrder, treeRoot, rotated, } = model;
+    const { drawTree, showBranchLen, labelsAlignRight, drawNodeLabels, drawLabels, treeAreaWidth, showTreeOverview, treeOrder, treeRoot, rotated, } = model;
     return [
         subMenu('Layout', [
             radio('Phylogram', drawTree && showBranchLen, () => {
@@ -136,9 +136,6 @@ export function treeSubMenu(model) {
         toggle('Tree overview', showTreeOverview, arg => {
             model.setShowTreeOverview(arg);
         }),
-        toggle('Scale bar', showTreeScaleBar, arg => {
-            model.setShowTreeScaleBar(arg);
-        }),
         subMenu('Order', [
             ...treeOrders.map(order => radio(treeOrderLabels[order], treeOrder === order, () => {
                 model.setTreeOrder(order);

package/dist/components/header/menuBarItems.js.map

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package/dist/constants.d.ts

@@ -15,6 +15,14 @@ export declare const subFeatureRowHeight = 4;
 export declare const domainUnderlineHeight = 3;
 export declare const segmentFeatureTypes: Set<string>;
 export declare const segmentShades: string[];
+/**
+ * A site's feature type: CDD's GenPept `Site`, a Sequence Ontology `*_site`,
+ * InterPro's `Binding_site`, `Active_site` and `Conserved_site`, and UniProt's
+ * `Binding site`. A site is a set of scattered residues, often single columns
+ */
+export declare function isSiteType(featureType: string | undefined): boolean;
+export declare const domainFills: string[];
+export declare const siteFills: string[];
 export declare const defaultDrawMsaLetters = true;
 export declare const defaultScrollZoom = false;
 export declare const scrollZoomAxes: readonly ['both', 'horizontal', 'vertical'];
@@ -46,7 +54,6 @@ export declare const defaultDrawTree = true;
 export declare const defaultDrawNodeBubbles = true;
 export declare const defaultDrawNodeLabels = false;
 export declare const defaultShowTreeOverview = false;
-export declare const defaultShowTreeScaleBar = false;
 export declare const defaultOverviewHeight = 120;
 export declare const maxNeighborJoiningRows = 500;
 export declare const rowTintAlpha = 0.25;

package/dist/constants.js

@@ -20,8 +20,8 @@ export const subFeatureRowHeight = 4;
 // height of the bar the overlay draws under a row in letter-color mode
 export const domainUnderlineHeight = 3;
 // Feature types that are ordinal segments of one transcript. The overlay
-// alternates two shades across them and labels them by number, where a domain
-// type gets its own hue and legend row.
+// alternates two shades across them and labels them by number, and every other
+// type gets its own color and legend row.
 export const segmentFeatureTypes = new Set([
     'exon',
     'CDS',
@@ -32,6 +32,30 @@ export const segmentFeatureTypes = new Set([
 ]);
 // the two shades alternated across adjacent segments (exons)
 export const segmentShades = ['#9fb6d4', '#d4dcea'];
+/**
+ * A site's feature type: CDD's GenPept `Site`, a Sequence Ontology `*_site`,
+ * InterPro's `Binding_site`, `Active_site` and `Conserved_site`, and UniProt's
+ * `Binding site`. A site is a set of scattered residues, often single columns
+ */
+export function isSiteType(featureType) {
+    return !!featureType && /(^|[_ ])site$/i.test(featureType);
+}
+// A domain fills a span the residue letters draw over, so it takes a light
+// color, CIELAB L* 80 or more. A site marks a few residues inside a domain, so
+// it takes a dark one, L* 50 or less: a thin mark needs lightness contrast to
+// show on a fill, and hue alone gives none. Neither list holds a grey or a
+// magenta, which a structure view draws for uncolored chains and for the
+// hovered residue
+export const domainFills = [
+    '#b3cde3',
+    '#fed9a6',
+    '#ccebc5',
+    '#decbe4',
+    '#fbb4ae',
+    '#e5d8bd',
+    '#fddaec',
+];
+export const siteFills = ['#178867', '#c05402', '#7570b3', '#518318', '#906719'];
 export const defaultDrawMsaLetters = true;
 export const defaultScrollZoom = false;
 // Which cell dimensions a wheel zoom scales. 'horizontal' holds the row height,
@@ -93,7 +117,6 @@ export const defaultDrawTree = true;
 export const defaultDrawNodeBubbles = true;
 export const defaultDrawNodeLabels = false;
 export const defaultShowTreeOverview = false;
-export const defaultShowTreeScaleBar = false;
 export const defaultOverviewHeight = 120;
 // Neighbor joining does not run above this many rows. The distance matrix is
 // O(n^2*L) and the join loop O(n^3), both on the main thread with no progress

package/dist/constants.js.map

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

@@ -3,9 +3,10 @@
  * order, such as the list a scale asked for by name; without it the keys take
  * the ggplot palette of their own size. Beyond the colors available — a
  * gene-structure overlay with one feature per exon, or nine keys on an
- * eight-color palette — every key gets an evenly spaced HSL hue instead, so no
- * two keys share a color.
+ * eight-color palette — every key gets an evenly spaced hue instead, so no
+ * two keys share a color. The hues sit at CIELAB `lightness` where one is
+ * given, else at HSL lightness 60.
  */
-export declare function createPaletteMap(keys: string[], palette?: readonly string[]): {
+export declare function createPaletteMap(keys: string[], palette?: readonly string[], lightness?: number): {
     [k: string]: string;
 };

package/dist/createPaletteMap.js

@@ -1,22 +1,30 @@
-import { colord } from 'colord';
+import { colord, extend } from 'colord';
+import lchPlugin from 'colord/plugins/lch';
 import palettes from './ggplotPalettes.js';
+extend([lchPlugin]);
 /**
  * Creates a map from keys to colors. `palette` names the colors to take in
  * order, such as the list a scale asked for by name; without it the keys take
  * the ggplot palette of their own size. Beyond the colors available — a
  * gene-structure overlay with one feature per exon, or nine keys on an
- * eight-color palette — every key gets an evenly spaced HSL hue instead, so no
- * two keys share a color.
+ * eight-color palette — every key gets an evenly spaced hue instead, so no
+ * two keys share a color. The hues sit at CIELAB `lightness` where one is
+ * given, else at HSL lightness 60.
  */
-export function createPaletteMap(keys, palette) {
+export function createPaletteMap(keys, palette, lightness) {
     const n = keys.length;
     const colors = palette ?? palettes[n - 1];
     if (colors && n <= colors.length) {
         return Object.fromEntries(keys.map((key, i) => [key, colors[i]]));
     }
-    return Object.fromEntries(keys.map((key, i) => [
-        key,
-        colord({ h: (i * 360) / n, s: 60, l: 60 }).toHex(),
-    ]));
+    return Object.fromEntries(keys.map((key, i) => {
+        const h = (i * 360) / n;
+        return [
+            key,
+            (lightness === undefined
+                ? colord({ h, s: 60, l: 60 })
+                : colord({ l: lightness, c: 40, h })).toHex(),
+        ];
+    }));
 }
 //# sourceMappingURL=createPaletteMap.js.map

package/dist/createPaletteMap.js.map

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+{"version":3,"file":"createPaletteMap.js","sourceRoot":"","sources":["../src/createPaletteMap.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,MAAM,EAAE,MAAM,EAAE,MAAM,QAAQ,CAAA;AACvC,OAAO,SAAS,MAAM,oBAAoB,CAAA;AAE1C,OAAO,QAAQ,MAAM,qBAAqB,CAAA;AAE1C,MAAM,CAAC,CAAC,SAAS,CAAC,CAAC,CAAA;AAEnB;;;;;;;;GAQG;AACH,MAAM,UAAU,gBAAgB,CAC9B,IAAc,EACd,OAA2B,EAC3B,SAAkB;IAElB,MAAM,CAAC,GAAG,IAAI,CAAC,MAAM,CAAA;IACrB,MAAM,MAAM,GAAG,OAAO,IAAI,QAAQ,CAAC,CAAC,GAAG,CAAC,CAAC,CAAA;IACzC,IAAI,MAAM,IAAI,CAAC,IAAI,MAAM,CAAC,MAAM,EAAE,CAAC;QACjC,OAAO,MAAM,CAAC,WAAW,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,GAAG,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,GAAG,EAAE,MAAM,CAAC,CAAC,CAAE,CAAC,CAAC,CAAC,CAAA;IACpE,CAAC;IACD,OAAO,MAAM,CAAC,WAAW,CACvB,IAAI,CAAC,GAAG,CAAC,CAAC,GAAG,EAAE,CAAC,EAAE,EAAE;QAClB,MAAM,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAC,GAAG,CAAC,CAAA;QACvB,OAAO;YACL,GAAG;YACH,CAAC,SAAS,KAAK,SAAS;gBACtB,CAAC,CAAC,MAAM,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,EAAE,EAAE,CAAC,EAAE,EAAE,EAAE,CAAC;gBAC7B,CAAC,CAAC,MAAM,CAAC,EAAE,CAAC,EAAE,SAAS,EAAE,CAAC,EAAE,EAAE,EAAE,CAAC,EAAE,CAAC,CACrC,CAAC,KAAK,EAAE;SACV,CAAA;IACH,CAAC,CAAC,CACH,CAAA;AACH,CAAC"}

package/dist/index.d.ts

@@ -2,7 +2,7 @@ export { renderToSvg } from './renderToSvg.tsx';
 export type { ExportSvgOptions } from './renderToSvg.tsx';
 export { installHeadlessRenderEnv } from './headlessRenderEnv.ts';
 export { CHAR_WIDTH_RATIO } from './measureTextCanvas.ts';
-export { maxNeighborJoiningRows } from './constants.ts';
+export { isSiteType, maxNeighborJoiningRows } from './constants.ts';
 export { expandSpec, residueLabel } from './expandSpec.ts';
 export type { ColumnTrackShorthand, HighlightShorthand, MsaSpec, RegionShorthand, } from './expandSpec.ts';
 export { default as MSAView } from './components/Loading.tsx';

package/dist/index.js

@@ -14,7 +14,7 @@ export { installHeadlessRenderEnv } from './headlessRenderEnv.js';
 export { CHAR_WIDTH_RATIO } from './measureTextCanvas.js';
 // the row count above which calculateNeighborJoiningTreeFromMSA throws, for
 // hosts gating their own menu item
-export { maxNeighborJoiningRows } from './constants.js';
+export { isSiteType, maxNeighborJoiningRows } from './constants.js';
 // the short forms a link or a script can write a view in; see docs/layers.md
 export { expandSpec, residueLabel } from './expandSpec.js';
 export { default as MSAView } from './components/Loading.js';

package/dist/index.js.map

@@ -1 +1 @@
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package/dist/model/treeModel.d.ts

@@ -62,11 +62,6 @@ export declare function TreeModelF(): import("@jbrowse/mobx-state-tree").IModelT
      * subtree boxed. A click on it focuses the subtree under the pointer
      */
     showTreeOverview: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-    /**
-     * #property
-     * draw the branch-length scale bar above the tree of a phylogram
-     */
-    showTreeScaleBar: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     /**
      * #property
      * height of the tree overview band, px
@@ -113,10 +108,6 @@ export declare function TreeModelF(): import("@jbrowse/mobx-state-tree").IModelT
      * #action
      */
     setShowTreeOverview(arg: boolean): void;
-    /**
-     * #action
-     */
-    setShowTreeScaleBar(arg: boolean): void;
     /**
      * #action
      */

package/dist/model/treeModel.js

@@ -1,5 +1,5 @@
 import { types } from '@jbrowse/mobx-state-tree';
-import { defaultDrawLabels, defaultDrawNodeBubbles, defaultDrawNodeLabels, defaultDrawTree, defaultLabelsAlignRight, defaultOverviewHeight, defaultShowBranchLen, defaultTreeOrder, defaultShowTreeOverview, defaultShowTreeScaleBar, treeOrders, } from '../constants.js';
+import { defaultDrawLabels, defaultDrawNodeBubbles, defaultDrawNodeLabels, defaultDrawTree, defaultLabelsAlignRight, defaultOverviewHeight, defaultShowBranchLen, defaultTreeOrder, defaultShowTreeOverview, treeOrders, } from '../constants.js';
 import { stripDefault } from '../stripDefault.js';
 /**
  * #stateModel Tree
@@ -66,11 +66,6 @@ export function TreeModelF() {
          * subtree boxed. A click on it focuses the subtree under the pointer
          */
         showTreeOverview: stripDefault(types.boolean, defaultShowTreeOverview),
-        /**
-         * #property
-         * draw the branch-length scale bar above the tree of a phylogram
-         */
-        showTreeScaleBar: stripDefault(types.boolean, defaultShowTreeScaleBar),
         /**
          * #property
          * height of the tree overview band, px
@@ -137,12 +132,6 @@ export function TreeModelF() {
         setShowTreeOverview(arg) {
             self.showTreeOverview = arg;
         },
-        /**
-         * #action
-         */
-        setShowTreeScaleBar(arg) {
-            self.showTreeScaleBar = arg;
-        },
         /**
          * #action
          */

package/dist/model/treeModel.js.map

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package/dist/model.d.ts

@@ -50,7 +50,7 @@ type FeaturePanelScale = Omit<ResolvedFeaturePanel, 'id' | 'width' | 'offsetX' |
  */
 declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
     maxInlineSnapshotBytes?: number;
-}): import("@jbrowse/mobx-state-tree").IModelType<Omit<Omit<Omit<{}, "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "showTreeScaleBar" | "treeAreaWidth" | "treeOrder" | "treeWidth"> & {
+}): import("@jbrowse/mobx-state-tree").IModelType<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>>;
@@ -61,7 +61,6 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
     drawNodeBubbles: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     drawNodeLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     showTreeOverview: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-    showTreeScaleBar: 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]>;
 }, "bgColor" | "colorSchemeName" | "customColorScheme" | "msaFormat" | "showColumnStats"> & {
     bgColor: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
@@ -668,7 +667,6 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
     setDrawNodeBubbles(arg: boolean): void;
     setDrawNodeLabels(arg: boolean): void;
     setShowTreeOverview(arg: boolean): void;
-    setShowTreeScaleBar(arg: boolean): void;
     setDrawLabels(arg: boolean): void;
 } & {
     setColorSchemeName(name: string): void;
@@ -1760,9 +1758,9 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
 } & {
     /**
      * #getter
-     * the branch-length scale bar over the tree, undefined while
-     * `showTreeScaleBar` is off, in cladogram mode, or when the tree area is
-     * too narrow for one
+     * the branch-length scale bar over the tree, the guide of its branch-length
+     * scale: undefined in cladogram mode, with the tree off, or when the tree
+     * area is too narrow for one
      */
     readonly treeScaleBar: {
         step: number;
@@ -2076,12 +2074,15 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
     /**
      * #getter
      * categorical feature types (InterPro domains and the like) that each get
-     * their own color and a legend entry, in palette order: grouped by
-     * feature type, types in the order they first appear. A GenPept
-     * record's CDD Sites follow every Region, so the palette spends the
-     * colors after the domains' on the sites inside them
+     * their own color and a legend entry
      */
     readonly categoricalDomainTypes: Annotation[];
+    /**
+     * #getter
+     * accession -> fill: segments alternate two shades, a domain takes a
+     * light color and a site a dark one, so a site's residues stand out on
+     * the domain around them
+     */
     readonly fillPalette: {
         [x: string]: string;
     };
@@ -2440,7 +2441,6 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
     drawNodeBubbles: boolean;
     drawNodeLabels: boolean;
     showTreeOverview: boolean;
-    showTreeScaleBar: boolean;
     overviewHeight: number;
     columnTracks: ColumnTrackSpec[];
     id: string;
@@ -2580,7 +2580,6 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
     drawNodeBubbles: boolean;
     drawNodeLabels: boolean;
     showTreeOverview: boolean;
-    showTreeScaleBar: boolean;
     overviewHeight: number;
     columnTracks?: undefined;
     id: string;

package/dist/model.js

@@ -13,7 +13,7 @@ import { packDomainLanes } from './components/msa/packDomainLanes.js';
 import { visibleColRange } from './components/msa/visibleColRange.js';
 import { cladeGutterWidth } from './components/tree/cladeBrackets.js';
 import { scaleBarLength } from './components/tree/scaleBar.js';
-import { defaultAllowedGappyness, defaultColWidth, defaultColorSchemeName, defaultCurrentAlignment, defaultDrawMsaLetters, defaultHeight, defaultHideGaps, defaultRowHeight, defaultScrollX, defaultScrollY, defaultScrollZoom, defaultScrollZoomAxis, defaultShowDomainLegend, defaultShowDomains, defaultSubFeatureRows, fontSizeFor, labelFitFontSize, maxCellSize, maxFitTreeWidth, maxTreeAreaShare, maxInlineSnapshotBytes as defaultMaxInlineSnapshotBytes, maxNeighborJoiningRows, minColWidth, minLetterColWidth, minLetterRowHeight, minRowHeight, minTreeWidth, pxPerTreeDepth, resizeHandleWidth, rowPanelHeaderHeight, rowTintAlpha, scrollZoomAxes, segmentFeatureTypes, segmentShades, settingsPanelWidth, treeScaleBarHeight, } from './constants.js';
+import { defaultAllowedGappyness, defaultColWidth, defaultColorSchemeName, defaultCurrentAlignment, defaultDrawMsaLetters, defaultHeight, defaultHideGaps, defaultRowHeight, defaultScrollX, defaultScrollY, defaultScrollZoom, defaultScrollZoomAxis, defaultShowDomainLegend, defaultShowDomains, domainFills, defaultSubFeatureRows, fontSizeFor, labelFitFontSize, maxCellSize, maxFitTreeWidth, maxTreeAreaShare, maxInlineSnapshotBytes as defaultMaxInlineSnapshotBytes, maxNeighborJoiningRows, minColWidth, minLetterColWidth, minLetterRowHeight, isSiteType, minRowHeight, minTreeWidth, pxPerTreeDepth, resizeHandleWidth, rowPanelHeaderHeight, rowTintAlpha, scrollZoomAxes, segmentFeatureTypes, segmentShades, settingsPanelWidth, siteFills, treeScaleBarHeight, } from './constants.js';
 import { createPaletteMap } from './createPaletteMap.js';
 import { exportFileName } from './exportFileName.js';
 import { featureField, featureName } from './featureFields.js';
@@ -116,7 +116,6 @@ export const preservedOnReset = new Set([
     'drawNodeBubbles',
     'drawNodeLabels',
     'showTreeOverview',
-    'showTreeScaleBar',
     'overviewHeight',
     'turnedOffTracks',
     'trackHeights',
@@ -2475,14 +2474,11 @@ function stateModelFactory({ maxInlineSnapshotBytes = defaultMaxInlineSnapshotBy
         .views(self => ({
         /**
          * #getter
-         * the branch-length scale bar over the tree, undefined while
-         * `showTreeScaleBar` is off, in cladogram mode, or when the tree area is
-         * too narrow for one
+         * the branch-length scale bar over the tree, the guide of its branch-length
+         * scale: undefined in cladogram mode, with the tree off, or when the tree
+         * area is too narrow for one
          */
         get treeScaleBar() {
-            if (!self.showTreeScaleBar) {
-                return undefined;
-            }
             return scaleBarLength(self.pxPerBranchLength, self.effectiveTreeAreaWidth - self.marginLeft * 2);
         },
         /**
@@ -3059,23 +3055,30 @@ function stateModelFactory({ maxInlineSnapshotBytes = defaultMaxInlineSnapshotBy
         /**
          * #getter
          * categorical feature types (InterPro domains and the like) that each get
-         * their own color and a legend entry, in palette order: grouped by
-         * feature type, types in the order they first appear. A GenPept
-         * record's CDD Sites follow every Region, so the palette spends the
-         * colors after the domains' on the sites inside them
+         * their own color and a legend entry
          */
         get categoricalDomainTypes() {
-            const types = [...self.annotationTypes.values()].filter(d => !segmentFeatureTypes.has(d.featureType ?? ''));
-            const typeOrder = [...new Set(types.map(d => d.featureType))];
-            return types.toSorted((a, b) => typeOrder.indexOf(a.featureType) - typeOrder.indexOf(b.featureType));
+            return [...self.annotationTypes.values()].filter(d => !segmentFeatureTypes.has(d.featureType ?? ''));
         },
+        /**
+         * #getter
+         * accession -> fill: segments alternate two shades, a domain takes a
+         * light color and a site a dark one, so a site's residues stand out on
+         * the domain around them
+         */
         get fillPalette() {
             const segments = Object.fromEntries(this.segmentDomainTypes.map((d, i) => [
                 d.accession,
                 segmentShades[i % segmentShades.length],
             ]));
-            const categorical = createPaletteMap(this.categoricalDomainTypes.map(d => d.accession));
-            return { ...segments, ...categorical };
+            const accessions = (site) => this.categoricalDomainTypes
+                .filter(d => isSiteType(d.featureType) === site)
+                .map(d => d.accession);
+            return {
+                ...segments,
+                ...createPaletteMap(accessions(false), domainFills, 85),
+                ...createPaletteMap(accessions(true), siteFills, 45),
+            };
         },
         /**
          * #getter