react-msaview 5.4.1 → 5.6.0

package/dist/components/tree/renderTreeCanvas.d.ts

@@ -1,27 +1,8 @@
+import type { ClickMapIndex } from './clickMap.ts';
 import type { MsaViewModel } from '../../model.ts';
 import type { RenderCtx } from '../renderCtx.ts';
 import type { Theme } from '@mui/material';
 export declare const padding = 600;
-interface ClickEntry {
-    name: string;
-    id: string;
-    branch?: boolean;
-    minX: number;
-    maxX: number;
-    minY: number;
-    maxY: number;
-}
-interface ClickMapIndex {
-    clear(): void;
-    insert(entry: ClickEntry): void;
-    finish(): void;
-    search(box: {
-        minX: number;
-        maxX: number;
-        minY: number;
-        maxY: number;
-    }): ClickEntry[];
-}
 export declare function renderTree({ offsetY, ctx, model, theme, maxBranchLen, maxDepthToLeaf, blockSizeYOverride, }: {
     offsetY: number;
     ctx: RenderCtx;
@@ -69,4 +50,3 @@ export declare function renderTreeCanvas({ model, clickMap, ctx, offsetY, theme,
     highResScaleFactorOverride?: number;
     blockSizeYOverride?: number;
 }): void;
-export {};

package/dist/components/tree/renderTreeCanvas.js

@@ -4,6 +4,11 @@ export const padding = 600;
 const extendBounds = 5;
 const radius = 2.5;
 const d = radius * 2;
+// whether a node's row-center y falls within the block being drawn, padded by
+// extendBounds so bubbles/labels/triangles straddling the edge still render
+function inYBlock(y, offsetY, by) {
+    return y > offsetY - extendBounds && y < offsetY + by + extendBounds;
+}
 // Calculate node x-coordinate for both phylogram (with branch lengths) and cladogram (topology only) modes
 // For cladograms: x = (maxDepthToLeaf - nodeDepthToLeaf) / maxDepthToLeaf * maxWidth
 // This positions: leaves at maxWidth (rightmost), root at 0 (leftmost), internal nodes proportionally in between
@@ -53,7 +58,7 @@ export function renderCollapsedTriangles({ ctx, clickMap, offsetY, model, theme,
         if (collapsed.includes(id)) {
             const apexX = getNodeX(node, showBranchLen, maxBranchLen, maxDepthToLeaf);
             const y = node.x;
-            const inBlock = y > offsetY - extendBounds && y < offsetY + by + extendBounds;
+            const inBlock = inYBlock(y, offsetY, by);
             // in cladogram mode the hidden tips align at the right edge, otherwise use
             // the branch-length extent recorded in the model's hierarchy getter
             const baseX = showBranchLen
@@ -104,9 +109,7 @@ export function renderNodeBubbles({ ctx, clickMap, offsetY, model, maxBranchLen,
         const { data } = node;
         const y = node.x;
         const { id, name } = data;
-        if (node.height >= 1 &&
-            y > offsetY - extendBounds &&
-            y < offsetY + by + extendBounds) {
+        if (node.height >= 1 && inYBlock(y, offsetY, by)) {
             const isCollapsed = collapsed.includes(id);
             ctx.strokeStyle = 'black';
             ctx.fillStyle = isCollapsed ? 'black' : 'white';
@@ -148,9 +151,7 @@ export function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, maxBran
         // a collapsed clade is drawn as a triangle + tip count; suppress its leaf
         // label when the "name" is just the auto-generated internal-node id
         const isAnonymousCollapsed = collapsed.includes(id) && name === id;
-        if (!isAnonymousCollapsed &&
-            y > offsetY - extendBounds &&
-            y < offsetY + by + extendBounds) {
+        if (!isAnonymousCollapsed && inYBlock(y, offsetY, by)) {
             // note: +rowHeight/4 matches with -rowHeight/4 in msa
             const yp = y + fontSize / 4;
             let xp = 0;

package/dist/components/tree/renderTreeCanvas.js.map

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

@@ -8,6 +8,9 @@ export declare const defaultShowDomains = false;
 export declare const defaultHideGaps = true;
 export declare const defaultAllowedGappyness = 100;
 export declare const defaultSubFeatureRows = false;
+export declare const subFeatureRowHeight = 4;
+export declare const segmentFeatureTypes: Set<string>;
+export declare const segmentShades: string[];
 export declare const defaultDrawMsaLetters = true;
 export declare const defaultScrollZoom = false;
 export declare const minColWidth = 0.2;
@@ -15,6 +18,7 @@ export declare const minRowHeight = 1;
 export declare const maxCellSize = 80;
 export declare const defaultBgColor = true;
 export declare const defaultColorSchemeName = "maeditor";
+export declare const defaultShowColumnStats = true;
 export declare const defaultDrawLabels = true;
 export declare const defaultLabelsAlignRight = false;
 export declare const defaultTreeAreaWidth = 400;

package/dist/constants.js

@@ -9,6 +9,22 @@ export const defaultShowDomains = false;
 export const defaultHideGaps = true;
 export const defaultAllowedGappyness = 100;
 export const defaultSubFeatureRows = false;
+// row height for each stacked feature when subFeatureRows is on
+export const subFeatureRowHeight = 4;
+// Feature types that are ordinal *segments* of a single transcript (exons and
+// the like) rather than categorical domains. Their identity is their position,
+// so the overlay alternates two shades to mark boundaries and labels them by
+// number, instead of assigning every one a distinct hue + legend row.
+export const segmentFeatureTypes = new Set([
+    'exon',
+    'CDS',
+    'five_prime_UTR',
+    'three_prime_UTR',
+    'UTR',
+    'intron',
+]);
+// the two shades alternated across adjacent segments (exons)
+export const segmentShades = ['#9fb6d4', '#d4dcea'];
 export const defaultDrawMsaLetters = true;
 export const defaultScrollZoom = false;
 // Zoom limits, px per cell. maxCellSize caps both smooth zoom and the stepwise
@@ -20,6 +36,7 @@ export const maxCellSize = 80;
 // MSA model defaults
 export const defaultBgColor = true;
 export const defaultColorSchemeName = 'maeditor';
+export const defaultShowColumnStats = true;
 // Tree model defaults
 export const defaultDrawLabels = true;
 export const defaultLabelsAlignRight = false;

package/dist/constants.js.map

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+{"version":3,"file":"constants.js","sourceRoot":"","sources":["../src/constants.ts"],"names":[],"mappings":"AAAA,sBAAsB;AACtB,MAAM,CAAC,MAAM,gBAAgB,GAAG,EAAE,CAAA;AAClC,MAAM,CAAC,MAAM,eAAe,GAAG,EAAE,CAAA;AACjC,MAAM,CAAC,MAAM,aAAa,GAAG,GAAG,CAAA;AAChC,MAAM,CAAC,MAAM,cAAc,GAAG,CAAC,CAAA;AAC/B,MAAM,CAAC,MAAM,cAAc,GAAG,CAAC,CAAA;AAC/B,MAAM,CAAC,MAAM,uBAAuB,GAAG,CAAC,CAAA;AACxC,MAAM,CAAC,MAAM,kBAAkB,GAAG,KAAK,CAAA;AACvC,MAAM,CAAC,MAAM,eAAe,GAAG,IAAI,CAAA;AACnC,MAAM,CAAC,MAAM,uBAAuB,GAAG,GAAG,CAAA;AAC1C,MAAM,CAAC,MAAM,qBAAqB,GAAG,KAAK,CAAA;AAC1C,gEAAgE;AAChE,MAAM,CAAC,MAAM,mBAAmB,GAAG,CAAC,CAAA;AAEpC,8EAA8E;AAC9E,+EAA+E;AAC/E,6EAA6E;AAC7E,sEAAsE;AACtE,MAAM,CAAC,MAAM,mBAAmB,GAAG,IAAI,GAAG,CAAC;IACzC,MAAM;IACN,KAAK;IACL,gBAAgB;IAChB,iBAAiB;IACjB,KAAK;IACL,QAAQ;CACT,CAAC,CAAA;AAEF,6DAA6D;AAC7D,MAAM,CAAC,MAAM,aAAa,GAAG,CAAC,SAAS,EAAE,SAAS,CAAC,CAAA;AACnD,MAAM,CAAC,MAAM,qBAAqB,GAAG,IAAI,CAAA;AACzC,MAAM,CAAC,MAAM,iBAAiB,GAAG,KAAK,CAAA;AAEtC,+EAA+E;AAC/E,iFAAiF;AACjF,0BAA0B;AAC1B,MAAM,CAAC,MAAM,WAAW,GAAG,GAAG,CAAA;AAC9B,MAAM,CAAC,MAAM,YAAY,GAAG,CAAC,CAAA;AAC7B,MAAM,CAAC,MAAM,WAAW,GAAG,EAAE,CAAA;AAE7B,qBAAqB;AACrB,MAAM,CAAC,MAAM,cAAc,GAAG,IAAI,CAAA;AAClC,MAAM,CAAC,MAAM,sBAAsB,GAAG,UAAU,CAAA;AAChD,MAAM,CAAC,MAAM,sBAAsB,GAAG,IAAI,CAAA;AAE1C,sBAAsB;AACtB,MAAM,CAAC,MAAM,iBAAiB,GAAG,IAAI,CAAA;AACrC,MAAM,CAAC,MAAM,uBAAuB,GAAG,KAAK,CAAA;AAC5C,MAAM,CAAC,MAAM,oBAAoB,GAAG,GAAG,CAAA;AACvC,MAAM,CAAC,MAAM,gBAAgB,GAAG,GAAG,CAAA;AACnC,MAAM,CAAC,MAAM,oBAAoB,GAAG,IAAI,CAAA;AACxC,MAAM,CAAC,MAAM,eAAe,GAAG,IAAI,CAAA;AACnC,MAAM,CAAC,MAAM,sBAAsB,GAAG,IAAI,CAAA"}

package/dist/createPaletteMap.d.ts

@@ -1,6 +1,9 @@
 /**
- * Creates a map from keys to colors using ggplot-style palettes.
- * The palette is selected based on the number of keys.
+ * Creates a map from keys to colors. Up to the largest ggplot palette (8 keys)
+ * we use the hand-picked ggplot colors; beyond that — e.g. a gene-structure
+ * overlay with one feature per exon — we generate evenly spaced HSL hues so
+ * every key still gets a distinct, stable color instead of running off the end
+ * of the palette.
  */
 export declare function createPaletteMap(keys: string[]): {
     [k: string]: string;

package/dist/createPaletteMap.js

@@ -1,11 +1,21 @@
+import { colord } from 'colord';
 import palettes from "./ggplotPalettes.js";
 /**
- * Creates a map from keys to colors using ggplot-style palettes.
- * The palette is selected based on the number of keys.
+ * Creates a map from keys to colors. Up to the largest ggplot palette (8 keys)
+ * we use the hand-picked ggplot colors; beyond that — e.g. a gene-structure
+ * overlay with one feature per exon — we generate evenly spaced HSL hues so
+ * every key still gets a distinct, stable color instead of running off the end
+ * of the palette.
  */
 export function createPaletteMap(keys) {
-    const k = Math.min(keys.length - 1, palettes.length - 1);
-    const palette = palettes[k];
-    return Object.fromEntries(keys.map((key, i) => [key, palette[i]]));
+    const n = keys.length;
+    if (n <= palettes.length) {
+        const palette = palettes[n - 1];
+        return Object.fromEntries(keys.map((key, i) => [key, palette[i]]));
+    }
+    return Object.fromEntries(keys.map((key, i) => [
+        key,
+        colord({ h: (i * 360) / n, s: 60, l: 60 }).toHex(),
+    ]));
 }
 //# sourceMappingURL=createPaletteMap.js.map

package/dist/createPaletteMap.js.map

@@ -1 +1 @@
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+{"version":3,"file":"createPaletteMap.js","sourceRoot":"","sources":["../src/createPaletteMap.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,MAAM,EAAE,MAAM,QAAQ,CAAA;AAE/B,OAAO,QAAQ,MAAM,qBAAqB,CAAA;AAE1C;;;;;;GAMG;AACH,MAAM,UAAU,gBAAgB,CAAC,IAAc;IAC7C,MAAM,CAAC,GAAG,IAAI,CAAC,MAAM,CAAA;IACrB,IAAI,CAAC,IAAI,QAAQ,CAAC,MAAM,EAAE,CAAC;QACzB,MAAM,OAAO,GAAG,QAAQ,CAAC,CAAC,GAAG,CAAC,CAAE,CAAA;QAChC,OAAO,MAAM,CAAC,WAAW,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,GAAG,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,GAAG,EAAE,OAAO,CAAC,CAAC,CAAE,CAAC,CAAC,CAAC,CAAA;IACrE,CAAC;IACD,OAAO,MAAM,CAAC,WAAW,CACvB,IAAI,CAAC,GAAG,CAAC,CAAC,GAAG,EAAE,CAAC,EAAE,EAAE,CAAC;QACnB,GAAG;QACH,MAAM,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC,GAAG,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,EAAE,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC,KAAK,EAAE;KACnD,CAAC,CACH,CAAA;AACH,CAAC"}

package/dist/fetchUtils.d.ts

@@ -1,4 +1,5 @@
 import { fetchAndMaybeUnzipText } from '@jbrowse/core/util';
+import type { RpcStatus } from '@jbrowse/core/util';
 export interface FetchStatus {
     msg: string;
     url?: string;
@@ -7,7 +8,7 @@ export interface FetchStatus {
 type Filehandle = Parameters<typeof fetchAndMaybeUnzipText>[0];
 type ProgressFetcher = (loc: Filehandle, opts: {
     signal: AbortSignal;
-    statusCallback: (msg: string) => void;
+    statusCallback: (status: RpcStatus) => void;
 }) => Promise<string>;
 /**
  * Fetch text from a filehandle while reporting download/unzip progress through

package/dist/fetchUtils.js

@@ -1,4 +1,4 @@
-import { fetchAndMaybeUnzipText } from '@jbrowse/core/util';
+import { fetchAndMaybeUnzipText, statusMessageText } from '@jbrowse/core/util';
 /**
  * Fetch text from a filehandle while reporting download/unzip progress through
  * setStatus, and wiring a Cancel handler that aborts the underlying request.
@@ -10,7 +10,8 @@ export async function fetchTextWithProgress(loc, setStatus, fetcher = fetchAndMa
     try {
         return await fetcher(loc, {
             signal: controller.signal,
-            statusCallback: msg => {
+            statusCallback: status => {
+                const msg = statusMessageText(status);
                 setStatus(msg
                     ? {
                         msg,

package/dist/fetchUtils.js.map

@@ -1 +1 @@
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+{"version":3,"file":"fetchUtils.js","sourceRoot":"","sources":["../src/fetchUtils.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,sBAAsB,EAAE,iBAAiB,EAAE,MAAM,oBAAoB,CAAA;AAiB9E;;;;;GAKG;AACH,MAAM,CAAC,KAAK,UAAU,qBAAqB,CACzC,GAAe,EACf,SAAyC,EACzC,UAA2B,sBAAsB;IAEjD,MAAM,UAAU,GAAG,IAAI,eAAe,EAAE,CAAA;IACxC,IAAI,CAAC;QACH,OAAO,MAAM,OAAO,CAAC,GAAG,EAAE;YACxB,MAAM,EAAE,UAAU,CAAC,MAAM;YACzB,cAAc,EAAE,MAAM,CAAC,EAAE;gBACvB,MAAM,GAAG,GAAG,iBAAiB,CAAC,MAAM,CAAC,CAAA;gBACrC,SAAS,CACP,GAAG;oBACD,CAAC,CAAC;wBACE,GAAG;wBACH,QAAQ,EAAE,GAAG,EAAE;4BACb,UAAU,CAAC,KAAK,EAAE,CAAA;wBACpB,CAAC;qBACF;oBACH,CAAC,CAAC,SAAS,CACd,CAAA;YACH,CAAC;SACF,CAAC,CAAA;IACJ,CAAC;YAAS,CAAC;QACT,SAAS,CAAC,SAAS,CAAC,CAAA;IACtB,CAAC;AACH,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,OAAO,CAAC,GAAW,EAAE,IAAkB;IAC3D,MAAM,QAAQ,GAAG,MAAM,KAAK,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;IAEvC,IAAI,CAAC,QAAQ,CAAC,EAAE,EAAE,CAAC;QACjB,MAAM,IAAI,KAAK,CACb,QAAQ,QAAQ,CAAC,MAAM,aAAa,GAAG,IAAI,MAAM,QAAQ,CAAC,IAAI,EAAE,EAAE,CACnE,CAAA;IACH,CAAC;IAED,OAAO,QAAQ,CAAA;AACjB,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,SAAS,CAAC,GAAW,EAAE,IAAkB;IAC7D,MAAM,QAAQ,GAAG,MAAM,OAAO,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;IACzC,OAAO,QAAQ,CAAC,IAAI,EAAE,CAAA;AACxB,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,SAAS,CAAI,GAAW,EAAE,IAAkB;IAChE,MAAM,QAAQ,GAAG,MAAM,OAAO,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;IACzC,OAAO,QAAQ,CAAC,IAAI,EAAO,CAAA;AAC7B,CAAC;AAED,MAAM,UAAU,OAAO,CAAC,IAAY,EAAE,MAAoB;IACxD,OAAO,IAAI,OAAO,CAAO,CAAC,OAAO,EAAE,MAAM,EAAE,EAAE;QAC3C,IAAI,MAAM,EAAE,OAAO,EAAE,CAAC;YACpB,MAAM,CAAC,IAAI,YAAY,CAAC,SAAS,EAAE,YAAY,CAAC,CAAC,CAAA;QACnD,CAAC;aAAM,CAAC;YACN,MAAM,EAAE,GAAG,UAAU,CAAC,OAAO,EAAE,IAAI,CAAC,CAAA;YACpC,MAAM,EAAE,gBAAgB,CAAC,OAAO,EAAE,GAAG,EAAE;gBACrC,YAAY,CAAC,EAAE,CAAC,CAAA;gBAChB,MAAM,CAAC,IAAI,YAAY,CAAC,SAAS,EAAE,YAAY,CAAC,CAAC,CAAA;YACnD,CAAC,CAAC,CAAA;QACJ,CAAC;IACH,CAAC,CAAC,CAAA;AACJ,CAAC;AAED,MAAM,UAAU,YAAY,CAAC,CAAU;IACrC,OAAO,CAAC,YAAY,YAAY,IAAI,CAAC,CAAC,IAAI,KAAK,YAAY,CAAA;AAC7D,CAAC"}

package/dist/index.d.ts

@@ -2,7 +2,7 @@ export { renderToSvg } from './renderToSvg.tsx';
 export { default as MSAView } from './components/Loading.tsx';
 export { default as MSAViewer } from './components/MSAViewer.tsx';
 export { type MsaViewModel, default as MSAModelF } from './model.ts';
-export type { MSAParserType } from 'msa-parsers';
+export type { MSAFormat, MSAParserType } from 'msa-parsers';
 export type { HierarchyNode } from './hierarchy.ts';
 export type { InterProScanResults } from './launchInterProScan.ts';
 export type { Accession, BasicTrack, BasicTrackModel, Node, NodeWithIds, NodeWithIdsAndLength, TextTrackModel, } from './types.ts';

package/dist/launchInterProScan.d.ts

@@ -6,11 +6,13 @@ export interface InterProScanResults {
                 name: string;
                 description: string;
                 accession: string;
+                featureType?: string;
             };
         };
         locations: {
             start: number;
             end: number;
+            strand?: number;
         }[];
     }[];
     xref: {

package/dist/launchInterProScan.js.map

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

@@ -3,8 +3,27 @@ import type { MSAFormat } from 'msa-parsers';
  * #stateModel MSAModel
  */
 export declare function MSAModelF(): import("@jbrowse/mobx-state-tree").IModelType<{
-    bgColor: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    colorSchemeName: import("@jbrowse/mobx-state-tree").IType<string | undefined, string, string>;
+    /**
+     * #property
+     * draw MSA tiles with a background color
+     */
+    bgColor: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    /**
+     * #property
+     * default color scheme name
+     */
+    colorSchemeName: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+    /**
+     * #property
+     * show a per-column statistics tooltip (consensus, conservation, gaps,
+     * residue distribution) while hovering the alignment
+     */
+    showColumnStats: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    /**
+     * #property
+     * force the MSA data to be parsed as a specific format instead of relying
+     * on auto-detection (which is ambiguous between e.g. fasta and a3m)
+     */
     msaFormat: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<MSAFormat>>;
 }, {
     /**
@@ -16,6 +35,10 @@ export declare function MSAModelF(): import("@jbrowse/mobx-state-tree").IModelTy
      * #action
      */
     setBgColor(arg: boolean): void;
+    /**
+     * #action
+     */
+    setShowColumnStats(arg: boolean): void;
     /**
      * #action
      * force a specific MSA parser, or pass undefined to auto-detect

package/dist/model/msaModel.js

@@ -1,5 +1,5 @@
 import { types } from '@jbrowse/mobx-state-tree';
-import { defaultBgColor, defaultColorSchemeName } from "../constants.js";
+import { defaultBgColor, defaultColorSchemeName, defaultShowColumnStats, } from "../constants.js";
 const msaFormats = ['stockholm', 'a3m', 'fasta', 'emf', 'clustal'];
 /**
  * #stateModel MSAModel
@@ -11,12 +11,18 @@ export function MSAModelF() {
          * #property
          * draw MSA tiles with a background color
          */
-        bgColor: defaultBgColor,
+        bgColor: types.stripDefault(types.boolean, defaultBgColor),
         /**
          * #property
          * default color scheme name
          */
-        colorSchemeName: defaultColorSchemeName,
+        colorSchemeName: types.stripDefault(types.string, defaultColorSchemeName),
+        /**
+         * #property
+         * show a per-column statistics tooltip (consensus, conservation, gaps,
+         * residue distribution) while hovering the alignment
+         */
+        showColumnStats: types.stripDefault(types.boolean, defaultShowColumnStats),
         /**
          * #property
          * force the MSA data to be parsed as a specific format instead of relying
@@ -38,6 +44,12 @@ export function MSAModelF() {
         setBgColor(arg) {
             self.bgColor = arg;
         },
+        /**
+         * #action
+         */
+        setShowColumnStats(arg) {
+            self.showColumnStats = arg;
+        },
         /**
          * #action
          * force a specific MSA parser, or pass undefined to auto-detect

package/dist/model/msaModel.js.map

@@ -1 +1 @@
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+{"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;AAIxB,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,KAAK,CAAC,YAAY,CAAC,KAAK,CAAC,OAAO,EAAE,cAAc,CAAC;QAE1D;;;WAGG;QACH,eAAe,EAAE,KAAK,CAAC,YAAY,CAAC,KAAK,CAAC,MAAM,EAAE,sBAAsB,CAAC;QAEzE;;;;WAIG;QACH,eAAe,EAAE,KAAK,CAAC,YAAY,CAAC,KAAK,CAAC,OAAO,EAAE,sBAAsB,CAAC;QAE1E;;;;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"}

package/dist/model/treeModel.d.ts

@@ -2,13 +2,50 @@
  * #stateModel Tree
  */
 export declare function TreeModelF(): import("@jbrowse/mobx-state-tree").IModelType<{
-    drawLabels: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    labelsAlignRight: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    /**
+     * #property
+     */
+    drawLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    /**
+     * #property
+     * right-align the labels
+     */
+    labelsAlignRight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    /**
+     * #property
+     * width of the area the tree is drawn in, px
+     */
     treeAreaWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+    /**
+     * #property
+     * width of the tree within the treeArea, px. automatically synced to
+     * fit within treeAreaWidth
+     */
     treeWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
-    showBranchLen: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    drawTree: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    drawNodeBubbles: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    /**
+     * #property
+     * use "branch length" e.g. evolutionary distance to draw tree branch
+     * lengths. if false, the layout is a "cladogram" that does not take into
+     * account evolutionary distances
+     */
+    showBranchLen: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    /**
+     * #property
+     * draw tree, boolean
+     */
+    drawTree: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    /**
+     * #property
+     * draw clickable node bubbles on the tree
+     */
+    drawNodeBubbles: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    /**
+     * #property
+     * auto-size treeAreaWidth to fit the row labels (plus the tree, if drawn)
+     * instead of using a fixed width. useful when there is no tree, so the
+     * label gutter isn't padded out to the default 400px
+     */
+    autoTreeAreaWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
 }, {
     /**
      * #action
@@ -28,6 +65,10 @@ export declare function TreeModelF(): import("@jbrowse/mobx-state-tree").IModelT
      * #action
      */
     setDrawTree(arg: boolean): void;
+    /**
+     * #action
+     */
+    setAutoTreeAreaWidth(arg: boolean): void;
     /**
      * #action
      */

package/dist/model/treeModel.js

@@ -9,40 +9,47 @@ export function TreeModelF() {
         /**
          * #property
          */
-        drawLabels: defaultDrawLabels,
+        drawLabels: types.stripDefault(types.boolean, defaultDrawLabels),
         /**
          * #property
          * right-align the labels
          */
-        labelsAlignRight: defaultLabelsAlignRight,
+        labelsAlignRight: types.stripDefault(types.boolean, defaultLabelsAlignRight),
         /**
          * #property
          * width of the area the tree is drawn in, px
          */
-        treeAreaWidth: types.optional(types.number, defaultTreeAreaWidth),
+        treeAreaWidth: types.stripDefault(types.number, defaultTreeAreaWidth),
         /**
          * #property
          * width of the tree within the treeArea, px. automatically synced to
          * fit within treeAreaWidth
          */
-        treeWidth: types.optional(types.number, defaultTreeWidth),
+        treeWidth: types.stripDefault(types.number, defaultTreeWidth),
         /**
          * #property
          * use "branch length" e.g. evolutionary distance to draw tree branch
          * lengths. if false, the layout is a "cladogram" that does not take into
          * account evolutionary distances
          */
-        showBranchLen: defaultShowBranchLen,
+        showBranchLen: types.stripDefault(types.boolean, defaultShowBranchLen),
         /**
          * #property
          * draw tree, boolean
          */
-        drawTree: defaultDrawTree,
+        drawTree: types.stripDefault(types.boolean, defaultDrawTree),
         /**
          * #property
          * draw clickable node bubbles on the tree
          */
-        drawNodeBubbles: defaultDrawNodeBubbles,
+        drawNodeBubbles: types.stripDefault(types.boolean, defaultDrawNodeBubbles),
+        /**
+         * #property
+         * auto-size treeAreaWidth to fit the row labels (plus the tree, if drawn)
+         * instead of using a fixed width. useful when there is no tree, so the
+         * label gutter isn't padded out to the default 400px
+         */
+        autoTreeAreaWidth: types.stripDefault(types.boolean, false),
     })
         .actions(self => ({
         /**
@@ -71,6 +78,12 @@ export function TreeModelF() {
         setDrawTree(arg) {
             self.drawTree = arg;
         },
+        /**
+         * #action
+         */
+        setAutoTreeAreaWidth(arg) {
+            self.autoTreeAreaWidth = arg;
+        },
         /**
          * #action
          */

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