react-msaview 5.5.0 → 5.6.0

package/dist/components/tree/TreeCanvasBlock.js

@@ -1,12 +1,12 @@
 import React, { useEffect, useRef, useState } from 'react';
+import { makeStyles } from '@jbrowse/core/util/tss-react';
 import { useTheme } from '@mui/material';
-import Flatbush from 'flatbush';
-import { autorun } from 'mobx';
 import { observer } from 'mobx-react';
-import { makeStyles } from 'tss-react/mui';
 import TreeBranchMenu from "./TreeBranchMenu.js";
 import TreeNodeMenu from "./TreeNodeMenu.js";
+import { ClickMapIndex } from "./clickMap.js";
 import { padding, renderTreeCanvas } from "./renderTreeCanvas.js";
+import { useCanvasAutorun } from "../../useCanvasAutorun.js";
 const useStyles = makeStyles()(theme => ({
     tooltip: {
         position: 'fixed',
@@ -23,38 +23,9 @@ const useStyles = makeStyles()(theme => ({
         textOverflow: 'ellipsis',
     },
 }));
-class ClickMapIndex {
-    flatbush = null;
-    entries = [];
-    clear() {
-        this.flatbush = null;
-        this.entries = [];
-    }
-    insert(entry) {
-        this.entries.push(entry);
-    }
-    finish() {
-        if (this.entries.length === 0) {
-            this.flatbush = null;
-        }
-        else {
-            this.flatbush = new Flatbush(this.entries.length);
-            for (const entry of this.entries) {
-                this.flatbush.add(entry.minX, entry.minY, entry.maxX, entry.maxY);
-            }
-            this.flatbush.finish();
-        }
-    }
-    search(box) {
-        return (this.flatbush
-            ?.search(box.minX, box.minY, box.maxX, box.maxY)
-            .map(i => this.entries[i]) ?? []);
-    }
-}
 const TreeCanvasBlock = observer(function ({ model, offsetY, }) {
     const { classes } = useStyles();
     const theme = useTheme();
-    const ref = useRef(null);
     const clickMap = useRef(new ClickMapIndex());
     const mouseoverRef = useRef(null);
     const [branchMenu, setBranchMenu] = useState();
@@ -66,21 +37,15 @@ const TreeCanvasBlock = observer(function ({ model, offsetY, }) {
     const height = blockSize;
     const w2 = width * highResScaleFactor;
     const h2 = height * highResScaleFactor;
-    useEffect(() => {
-        const ctx = ref.current?.getContext('2d');
-        if (!ctx) {
-            return;
-        }
-        return autorun(() => {
-            ctx.resetTransform();
-            ctx.clearRect(0, 0, (treeAreaWidth + padding) * highResScaleFactor, blockSize * highResScaleFactor);
-            renderTreeCanvas({
-                ctx,
-                model,
-                offsetY,
-                clickMap: clickMap.current,
-                theme,
-            });
+    const ref = useCanvasAutorun(ctx => {
+        ctx.resetTransform();
+        ctx.clearRect(0, 0, w2, h2);
+        renderTreeCanvas({
+            ctx,
+            model,
+            offsetY,
+            clickMap: clickMap.current,
+            theme,
         });
     }, [model, blockSize, highResScaleFactor, treeAreaWidth, offsetY, theme]);
     useEffect(() => {

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

@@ -1 +1 @@
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+{"version":3,"file":"TreeCanvasBlock.js","sourceRoot":"","sources":["../../../src/components/tree/TreeCanvasBlock.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,SAAS,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAE1D,OAAO,EAAE,UAAU,EAAE,MAAM,8BAA8B,CAAA;AACzD,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AACxC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,cAAc,MAAM,qBAAsB,CAAA;AACjD,OAAO,YAAY,MAAM,mBAAoB,CAAA;AAC7C,OAAO,EAAE,aAAa,EAAE,MAAM,eAAe,CAAA;AAC7C,OAAO,EAAE,OAAO,EAAE,gBAAgB,EAAE,MAAM,uBAAuB,CAAA;AACjE,OAAO,EAAE,gBAAgB,EAAE,MAAM,2BAA2B,CAAA;AAK5D,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,OAAO,EAAE;QACP,QAAQ,EAAE,OAAO;QACjB,aAAa,EAAE,MAAM;QACrB,MAAM,EAAE,KAAK;QACb,eAAe,EAAE,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC;QACxC,KAAK,EAAE,KAAK,CAAC,OAAO,CAAC,MAAM,CAAC,KAAK;QACjC,OAAO,EAAE,SAAS;QAClB,YAAY,EAAE,CAAC;QACf,QAAQ,EAAE,EAAE;QACZ,UAAU,EAAE,QAAQ;QACpB,QAAQ,EAAE,GAAG;QACb,QAAQ,EAAE,QAAQ;QAClB,YAAY,EAAE,UAAU;KACzB;CACF,CAAC,CAAC,CAAA;AASH,MAAM,eAAe,GAAG,QAAQ,CAAC,UAAU,EACzC,KAAK,EACL,OAAO,GAIR;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,KAAK,GAAG,QAAQ,EAAE,CAAA;IACxB,MAAM,QAAQ,GAAG,MAAM,CAAC,IAAI,aAAa,EAAE,CAAC,CAAA;IAC5C,MAAM,YAAY,GAAG,MAAM,CAAoB,IAAI,CAAC,CAAA;IACpD,MAAM,CAAC,UAAU,EAAE,aAAa,CAAC,GAAG,QAAQ,EAAe,CAAA;IAC3D,MAAM,CAAC,cAAc,EAAE,iBAAiB,CAAC,GAAG,QAAQ,EAAe,CAAA;IACnE,MAAM,CAAC,QAAQ,EAAE,WAAW,CAAC,GAAG,QAAQ,EAAc,CAAA;IACtD,MAAM,CAAC,WAAW,EAAE,cAAc,CAAC,GAAG,QAAQ,EAI1C,CAAA;IAEJ,MAAM,EAAE,OAAO,EAAE,aAAa,EAAE,SAAS,EAAE,kBAAkB,EAAE,GAAG,KAAK,CAAA;IAEvE,MAAM,KAAK,GAAG,aAAa,GAAG,OAAO,CAAA;IACrC,MAAM,MAAM,GAAG,SAAS,CAAA;IACxB,MAAM,EAAE,GAAG,KAAK,GAAG,kBAAkB,CAAA;IACrC,MAAM,EAAE,GAAG,MAAM,GAAG,kBAAkB,CAAA;IAEtC,MAAM,GAAG,GAAG,gBAAgB,CAC1B,GAAG,CAAC,EAAE;QACJ,GAAG,CAAC,cAAc,EAAE,CAAA;QACpB,GAAG,CAAC,SAAS,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,EAAE,EAAE,CAAC,CAAA;QAC3B,gBAAgB,CAAC;YACf,GAAG;YACH,KAAK;YACL,OAAO;YACP,QAAQ,EAAE,QAAQ,CAAC,OAAO;YAC1B,KAAK;SACN,CAAC,CAAA;IACJ,CAAC,EACD,CAAC,KAAK,EAAE,SAAS,EAAE,kBAAkB,EAAE,aAAa,EAAE,OAAO,EAAE,KAAK,CAAC,CACtE,CAAA;IAED,SAAS,CAAC,GAAG,EAAE;QACb,MAAM,GAAG,GAAG,YAAY,CAAC,OAAO,EAAE,UAAU,CAAC,IAAI,CAAC,CAAA;QAClD,IAAI,CAAC,GAAG,EAAE,CAAC;YACT,OAAM;QACR,CAAC;QAED,GAAG,CAAC,cAAc,EAAE,CAAA;QACpB,GAAG,CAAC,SAAS,CAAC,CAAC,EAAE,CAAC,EAAE,aAAa,GAAG,OAAO,EAAE,SAAS,CAAC,CAAA;QACvD,GAAG,CAAC,SAAS,CAAC,CAAC,EAAE,CAAC,OAAO,CAAC,CAAA;QAE1B,gDAAgD;QAChD,IAAI,QAAQ,EAAE,CAAC;YACb,MAAM,EAAE,IAAI,EAAE,IAAI,EAAE,IAAI,EAAE,IAAI,EAAE,GAAG,QAAQ,CAAA;YAE3C,GAAG,CAAC,SAAS,GAAG,iBAAiB,CAAA;YACjC,GAAG,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,EAAE,IAAI,GAAG,IAAI,EAAE,IAAI,GAAG,IAAI,CAAC,CAAA;QACpD,CAAC;IACH,CAAC,EAAE,CAAC,QAAQ,EAAE,OAAO,EAAE,SAAS,EAAE,aAAa,CAAC,CAAC,CAAA;IAEjD,SAAS,mBAAmB,CAAC,KAAuB;QAClD,MAAM,CAAC,GAAG,KAAK,CAAC,WAAW,CAAC,OAAO,CAAA;QACnC,MAAM,CAAC,GAAG,KAAK,CAAC,WAAW,CAAC,OAAO,CAAA;QAEnC,MAAM,CAAC,KAAK,CAAC,GAAG,QAAQ,CAAC,OAAO,CAAC,MAAM,CAAC;YACtC,IAAI,EAAE,CAAC;YACP,IAAI,EAAE,CAAC,GAAG,CAAC;YACX,IAAI,EAAE,CAAC,GAAG,OAAO;YACjB,IAAI,EAAE,CAAC,GAAG,CAAC,GAAG,OAAO;SACtB,CAAC,CAAA;QAEF,OAAO,KAAK,EAAE,MAAM;YAClB,CAAC,CAAC,EAAE,GAAG,KAAK,EAAE,CAAC,EAAE,KAAK,CAAC,OAAO,EAAE,CAAC,EAAE,KAAK,CAAC,OAAO,EAAE;YAClD,CAAC,CAAC,SAAS,CAAA;IACf,CAAC;IAED,SAAS,iBAAiB,CAAC,KAAuB;QAChD,MAAM,CAAC,GAAG,KAAK,CAAC,WAAW,CAAC,OAAO,CAAA;QACnC,MAAM,CAAC,GAAG,KAAK,CAAC,WAAW,CAAC,OAAO,CAAA;QACnC,MAAM,CAAC,KAAK,CAAC,GAAG,QAAQ,CAAC,OAAO,CAAC,MAAM,CAAC;YACtC,IAAI,EAAE,CAAC;YACP,IAAI,EAAE,CAAC,GAAG,CAAC;YACX,IAAI,EAAE,CAAC,GAAG,OAAO;YACjB,IAAI,EAAE,CAAC,GAAG,CAAC,GAAG,OAAO;SACtB,CAAC,CAAA;QAEF,OAAO,KAAK,IAAI,CAAC,KAAK,CAAC,MAAM;YAC3B,CAAC,CAAC,EAAE,GAAG,KAAK,EAAE,CAAC,EAAE,KAAK,CAAC,OAAO,EAAE,CAAC,EAAE,KAAK,CAAC,OAAO,EAAE;YAClD,CAAC,CAAC,SAAS,CAAA;IACf,CAAC;IACD,MAAM,KAAK,GAAG;QACZ,KAAK;QACL,MAAM;QACN,GAAG,EAAE,OAAO,GAAG,OAAO;QACtB,IAAI,EAAE,CAAC;QACP,QAAQ,EAAE,UAAU;KACZ,CAAA;IACV,OAAO,CACL;QACG,UAAU,EAAE,EAAE,CAAC,CAAC,CAAC,CAChB,oBAAC,cAAc,IACb,IAAI,EAAE,UAAU,EAChB,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,GAAG,EAAE;gBACZ,aAAa,CAAC,SAAS,CAAC,CAAA;YAC1B,CAAC,GACD,CACH,CAAC,CAAC,CAAC,IAAI;QAEP,cAAc,EAAE,EAAE,CAAC,CAAC,CAAC,CACpB,oBAAC,YAAY,IACX,IAAI,EAAE,cAAc,EACpB,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,GAAG,EAAE;gBACZ,iBAAiB,CAAC,SAAS,CAAC,CAAA;YAC9B,CAAC,GACD,CACH,CAAC,CAAC,CAAC,IAAI;QAER,gCACE,KAAK,EAAE,EAAE,EACT,MAAM,EAAE,EAAE,EACV,KAAK,EAAE,KAAK,EACZ,WAAW,EAAE,KAAK,CAAC,EAAE;gBACnB,IAAI,CAAC,GAAG,CAAC,OAAO,EAAE,CAAC;oBACjB,OAAM;gBACR,CAAC;gBAED,MAAM,WAAW,GAAG,iBAAiB,CAAC,KAAK,CAAC,CAAA;gBAC5C,MAAM,aAAa,GAAG,mBAAmB,CAAC,KAAK,CAAC,CAAA;gBAChD,MAAM,UAAU,GAAG,WAAW,IAAI,aAAa,CAAA;gBAE/C,GAAG,CAAC,OAAO,CAAC,KAAK,CAAC,MAAM,GAAG,UAAU,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,SAAS,CAAA;gBAC7D,WAAW,CAAC,WAAW,CAAC,CAAA,CAAC,kDAAkD;gBAE3E,mBAAmB;gBACnB,IAAI,UAAU,EAAE,CAAC;oBACf,cAAc,CAAC;wBACb,IAAI,EAAE,UAAU,CAAC,IAAI;wBACrB,CAAC,EAAE,KAAK,CAAC,OAAO;wBAChB,CAAC,EAAE,KAAK,CAAC,OAAO;qBACjB,CAAC,CAAA;gBACJ,CAAC;qBAAM,CAAC;oBACN,cAAc,CAAC,SAAS,CAAC,CAAA;gBAC3B,CAAC;gBAED,oDAAoD;gBACpD,IAAI,UAAU,EAAE,CAAC;oBACf,KAAK,CAAC,kBAAkB,CAAC,UAAU,CAAC,EAAE,CAAC,CAAA;oBAEvC,2EAA2E;oBAC3E,IAAI,WAAW,EAAE,IAAI,EAAE,CAAC;wBACtB,MAAM,QAAQ,GAAG,KAAK,CAAC,WAAW,C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package/dist/components/tree/clickMap.d.ts

@@ -0,0 +1,24 @@
+export interface ClickEntry {
+    name: string;
+    id: string;
+    branch?: boolean;
+    minX: number;
+    maxX: number;
+    minY: number;
+    maxY: number;
+}
+interface Box {
+    minX: number;
+    maxX: number;
+    minY: number;
+    maxY: number;
+}
+export declare class ClickMapIndex {
+    private flatbush;
+    private entries;
+    clear(): void;
+    insert(entry: ClickEntry): void;
+    finish(): void;
+    search(box: Box): ClickEntry[];
+}
+export {};

package/dist/components/tree/clickMap.js

@@ -0,0 +1,33 @@
+import Flatbush from 'flatbush';
+// Spatial index of clickable tree elements (leaf labels, node bubbles,
+// collapsed-clade triangles). Entries are collected during a render pass, then
+// finish() builds the Flatbush index queried by hit-testing.
+export class ClickMapIndex {
+    flatbush = null;
+    entries = [];
+    clear() {
+        this.flatbush = null;
+        this.entries = [];
+    }
+    insert(entry) {
+        this.entries.push(entry);
+    }
+    finish() {
+        if (this.entries.length === 0) {
+            this.flatbush = null;
+        }
+        else {
+            this.flatbush = new Flatbush(this.entries.length);
+            for (const entry of this.entries) {
+                this.flatbush.add(entry.minX, entry.minY, entry.maxX, entry.maxY);
+            }
+            this.flatbush.finish();
+        }
+    }
+    search(box) {
+        return (this.flatbush
+            ?.search(box.minX, box.minY, box.maxX, box.maxY)
+            .map(i => this.entries[i]) ?? []);
+    }
+}
+//# sourceMappingURL=clickMap.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"clickMap.js","sourceRoot":"","sources":["../../../src/components/tree/clickMap.ts"],"names":[],"mappings":"AAAA,OAAO,QAAQ,MAAM,UAAU,CAAA;AAmB/B,uEAAuE;AACvE,+EAA+E;AAC/E,6DAA6D;AAC7D,MAAM,OAAO,aAAa;IAChB,QAAQ,GAAoB,IAAI,CAAA;IAChC,OAAO,GAAiB,EAAE,CAAA;IAElC,KAAK;QACH,IAAI,CAAC,QAAQ,GAAG,IAAI,CAAA;QACpB,IAAI,CAAC,OAAO,GAAG,EAAE,CAAA;IACnB,CAAC;IAED,MAAM,CAAC,KAAiB;QACtB,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;IAC1B,CAAC;IAED,MAAM;QACJ,IAAI,IAAI,CAAC,OAAO,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAC9B,IAAI,CAAC,QAAQ,GAAG,IAAI,CAAA;QACtB,CAAC;aAAM,CAAC;YACN,IAAI,CAAC,QAAQ,GAAG,IAAI,QAAQ,CAAC,IAAI,CAAC,OAAO,CAAC,MAAM,CAAC,CAAA;YACjD,KAAK,MAAM,KAAK,IAAI,IAAI,CAAC,OAAO,EAAE,CAAC;gBACjC,IAAI,CAAC,QAAQ,CAAC,GAAG,CAAC,KAAK,CAAC,IAAI,EAAE,KAAK,CAAC,IAAI,EAAE,KAAK,CAAC,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,CAAA;YACnE,CAAC;YACD,IAAI,CAAC,QAAQ,CAAC,MAAM,EAAE,CAAA;QACxB,CAAC;IACH,CAAC;IAED,MAAM,CAAC,GAAQ;QACb,OAAO,CACL,IAAI,CAAC,QAAQ;YACX,EAAE,MAAM,CAAC,GAAG,CAAC,IAAI,EAAE,GAAG,CAAC,IAAI,EAAE,GAAG,CAAC,IAAI,EAAE,GAAG,CAAC,IAAI,CAAC;aAC/C,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,CAAE,CAAC,IAAI,EAAE,CACpC,CAAA;IACH,CAAC;CACF"}

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

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package/dist/constants.d.ts

@@ -18,6 +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

@@ -36,6 +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

@@ -1 +1 @@
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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/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/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
          */

package/dist/model/treeModel.js.map

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