react-msaview 6.1.0 → 6.1.1

package/dist/components/header/settingsMenuItems.js

@@ -51,7 +51,7 @@ export function treeSettingsMenuItems(model) {
         toggle('Show tree', drawTree, arg => {
             model.setDrawTree(arg);
         }),
-        toggle('Draw clickable bubbles on tree branches', drawNodeBubbles, arg => {
+        toggle('Draw bubbles on tree branches', drawNodeBubbles, arg => {
             model.setDrawNodeBubbles(arg);
         }),
         toggle('Tree labels align right', labelsAlignRight, arg => {

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

@@ -1 +1 @@
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+{"version":3,"file":"settingsMenuItems.js","sourceRoot":"","sources":["../../../src/components/header/settingsMenuItems.ts"],"names":[],"mappings":"AAGA,SAAS,MAAM,CAAC,KAAa,EAAE,OAAgB,EAAE,GAA2B;IAC1E,OAAO;QACL,KAAK;QACL,IAAI,EAAE,UAAmB;QACzB,OAAO;QACP,OAAO,EAAE,GAAG,EAAE;YACZ,GAAG,CAAC,CAAC,OAAO,CAAC,CAAA;QACf,CAAC;KACF,CAAA;AACH,CAAC;AAED,+EAA+E;AAC/E,+EAA+E;AAC/E,0CAA0C;AAC1C,SAAS,aAAa,CAAC,KAAmB;IACxC,MAAM,KAAK,GAAG,IAAI,GAAG,CAAC,KAAK,CAAC,cAAc,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC,CAAA;IAChE,OAAO,KAAK,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC,EAAE,KAAK,EAAE,EAAE,EAAE,EAAE,IAAI,EAAE,EAAE,EAAE,EAAE,CAClD,MAAM,CAAC,IAAI,EAAE,KAAK,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,GAAG,EAAE;QAC/B,KAAK,CAAC,WAAW,CAAC,EAAE,CAAC,CAAA;IACvB,CAAC,CAAC,CACH,CAAA;AACH,CAAC;AAED,MAAM,UAAU,oBAAoB,CAAC,KAAmB;IACtD,MAAM,EAAE,cAAc,EAAE,QAAQ,EAAE,OAAO,EAAE,eAAe,EAAE,GAAG,KAAK,CAAA;IACpE,OAAO;QACL;YACE,KAAK,EAAE,QAAQ;YACf,IAAI,EAAE,SAAkB;YACxB,OAAO,EAAE,aAAa,CAAC,KAAK,CAAC;SAC9B;QACD,EAAE,IAAI,EAAE,SAAkB,EAAE;QAC5B,MAAM,CAAC,iCAAiC,EAAE,eAAe,EAAE,GAAG,CAAC,EAAE;YAC/D,KAAK,CAAC,kBAAkB,CAAC,GAAG,CAAC,CAAA;QAC/B,CAAC,CAAC;QACF,MAAM,CAAC,cAAc,EAAE,cAAc,EAAE,GAAG,CAAC,EAAE;YAC3C,KAAK,CAAC,iBAAiB,CAAC,GAAG,CAAC,CAAA;QAC9B,CAAC,CAAC;QACF,2EAA2E;QAC3E,wEAAwE;QACxE,MAAM,CAAC,8CAA8C,EAAE,CAAC,OAAO,EAAE,GAAG,CAAC,EAAE;YACrE,KAAK,CAAC,UAAU,CAAC,CAAC,GAAG,CAAC,CAAA;QACxB,CAAC,CAAC;QACF,MAAM,CAAC,8BAA8B,EAAE,QAAQ,EAAE,GAAG,CAAC,EAAE;YACrD,KAAK,CAAC,WAAW,CAAC,GAAG,CAAC,CAAA;QACxB,CAAC,CAAC;KACH,CAAA;AACH,CAAC;AAED,MAAM,UAAU,qBAAqB,CAAC,KAAmB;IACvD,MAAM,EACJ,QAAQ,EACR,aAAa,EACb,gBAAgB,EAChB,eAAe,EACf,UAAU,GACX,GAAG,KAAK,CAAA;IACT,OAAO;QACL,MAAM,CAAC,oBAAoB,EAAE,aAAa,EAAE,GAAG,CAAC,EAAE;YAChD,KAAK,CAAC,gBAAgB,CAAC,GAAG,CAAC,CAAA;QAC7B,CAAC,CAAC;QACF,MAAM,CAAC,WAAW,EAAE,QAAQ,EAAE,GAAG,CAAC,EAAE;YAClC,KAAK,CAAC,WAAW,CAAC,GAAG,CAAC,CAAA;QACxB,CAAC,CAAC;QACF,MAAM,CAAC,+BAA+B,EAAE,eAAe,EAAE,GAAG,CAAC,EAAE;YAC7D,KAAK,CAAC,kBAAkB,CAAC,GAAG,CAAC,CAAA;QAC/B,CAAC,CAAC;QACF,MAAM,CAAC,yBAAyB,EAAE,gBAAgB,EAAE,GAAG,CAAC,EAAE;YACxD,KAAK,CAAC,mBAAmB,CAAC,GAAG,CAAC,CAAA;QAChC,CAAC,CAAC;QACF,MAAM,CAAC,aAAa,EAAE,UAAU,EAAE,GAAG,CAAC,EAAE;YACtC,KAAK,CAAC,aAAa,CAAC,GAAG,CAAC,CAAA;QAC1B,CAAC,CAAC;KACH,CAAA;AACH,CAAC"}

package/dist/components/tree/renderTreeCanvas.js

@@ -103,7 +103,9 @@ function renderCollapsedTriangles({ ctx, clickMap, offsetY, model, theme, tipX,
         }
     });
 }
-function renderNodeBubbles({ ctx, clickMap, offsetY, model, tipX, maxDepthToLeaf, blockSizeYOverride, collapsedSet, }) {
+// the bubbles are click targets whether or not they are painted, so this pass
+// always runs and `draw` only decides whether it also strokes the circles
+function renderNodeBubbles({ ctx, clickMap, offsetY, model, tipX, maxDepthToLeaf, blockSizeYOverride, collapsedSet, draw, }) {
     const { hierarchy, showBranchLenEffective: showBranchLen, blockSize, marginLeft: ml, } = model;
     const by = blockSizeYOverride ?? blockSize;
     forEachDescendant(hierarchy, node => {
@@ -116,12 +118,14 @@ function renderNodeBubbles({ ctx, clickMap, offsetY, model, tipX, maxDepthToLeaf
         const { id, name } = data;
         if (node.height >= 1 && inYBlock(y, offsetY, by)) {
             const isCollapsed = collapsedSet.has(id);
-            ctx.strokeStyle = 'black';
-            ctx.fillStyle = isCollapsed ? 'black' : 'white';
-            ctx.beginPath();
-            ctx.arc(x, y, radius, 0, 2 * Math.PI);
-            ctx.fill();
-            ctx.stroke();
+            if (draw) {
+                ctx.strokeStyle = 'black';
+                ctx.fillStyle = isCollapsed ? 'black' : 'white';
+                ctx.beginPath();
+                ctx.arc(x, y, radius, 0, 2 * Math.PI);
+                ctx.fill();
+                ctx.stroke();
+            }
             // collapsed nodes get their click/hover target from the triangle pass,
             // which covers the apex bubble and carries a descriptive label
             if (!isCollapsed) {
@@ -254,18 +258,17 @@ export function renderTreeCanvas({ model, clickMap, ctx, offsetY, theme, highRes
             blockSizeYOverride,
             collapsedSet,
         });
-        if (drawNodeBubbles) {
-            renderNodeBubbles({
-                ctx,
-                offsetY,
-                clickMap,
-                model,
-                tipX,
-                maxDepthToLeaf,
-                blockSizeYOverride,
-                collapsedSet,
-            });
-        }
+        renderNodeBubbles({
+            ctx,
+            offsetY,
+            clickMap,
+            model,
+            tipX,
+            maxDepthToLeaf,
+            blockSizeYOverride,
+            collapsedSet,
+            draw: drawNodeBubbles,
+        });
     }
     if (showTreeText) {
         renderTreeLabels({

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

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

@@ -36,7 +36,7 @@ export declare function TreeModelF(): import("@jbrowse/mobx-state-tree").IModelT
     drawTree: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     /**
      * #property
-     * draw clickable node bubbles on the tree
+     * draw node bubbles on the tree; the branches stay clickable either way
      */
     drawNodeBubbles: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     /**

package/dist/model/treeModel.js

@@ -41,7 +41,7 @@ export function TreeModelF() {
         drawTree: stripDefault(types.boolean, defaultDrawTree),
         /**
          * #property
-         * draw clickable node bubbles on the tree
+         * draw node bubbles on the tree; the branches stay clickable either way
          */
         drawNodeBubbles: stripDefault(types.boolean, defaultDrawNodeBubbles),
         /**

package/dist/version.d.ts

@@ -1 +1 @@
-export declare const version = "6.1.0";
+export declare const version = "6.1.1";

package/dist/version.js

@@ -1,2 +1,2 @@
-export const version = '6.1.0';
+export const version = '6.1.1';
 //# sourceMappingURL=version.js.map

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "react-msaview",
   "author": "Colin",
-  "version": "6.1.0",
+  "version": "6.1.1",
   "license": "MIT",
   "type": "module",
   "repository": {
@@ -43,8 +43,8 @@
     "@gmod/newick": "^1.0.0",
     "colord": "^2.9.3",
     "flatbush": "^4.6.2",
-    "@jbrowse/svgcanvas": "6.1.0",
-    "msa-parsers": "6.1.0"
+    "@jbrowse/svgcanvas": "6.1.1",
+    "msa-parsers": "6.1.1"
   },
   "scripts": {
     "clean": "rimraf dist bundle",

package/src/components/header/settingsMenuItems.ts

@@ -65,7 +65,7 @@ export function treeSettingsMenuItems(model: MsaViewModel): MenuItem[] {
     toggle('Show tree', drawTree, arg => {
       model.setDrawTree(arg)
     }),
-    toggle('Draw clickable bubbles on tree branches', drawNodeBubbles, arg => {
+    toggle('Draw bubbles on tree branches', drawNodeBubbles, arg => {
       model.setDrawNodeBubbles(arg)
     }),
     toggle('Tree labels align right', labelsAlignRight, arg => {

package/src/components/tree/renderTreeCanvas.test.ts

@@ -2,6 +2,7 @@ import { describe, expect, it } from 'vitest'
 
 import { calcDepthToLeaf, findMaxBranchLen } from '../../hierarchy.ts'
 import stateModelFactory from '../../model.ts'
+import { ClickMapIndex } from './clickMap.ts'
 import { getNodeX, renderTreeCanvas } from './renderTreeCanvas.ts'
 
 import type { HierarchyNode } from '../../hierarchy.ts'
@@ -174,3 +175,57 @@ describe('renderTreeCanvas horizontal extent', () => {
     expect(model.treeWidth).toBe(model.treeAreaWidth - 10 - model.marginLeft)
   })
 })
+
+describe('node bubble click targets', () => {
+  const bounds = { minX: 0, minY: 0, maxX: 10000, maxY: 10000 }
+
+  // "draw clickable bubbles" only controls the painting; the branches have to
+  // stay clickable with it off
+  function renderWithBubbles(drawNodeBubbles: boolean) {
+    const model = stateModelFactory().create({
+      type: 'MsaView',
+      data: { msa: '>a\nA\n>b\nA\n>c\nA\n>d\nA', tree: '((a,b),(c,d));' },
+    })
+    model.setWidth(1000)
+    model.setDrawLabels(false)
+    model.setDrawNodeBubbles(drawNodeBubbles)
+
+    let arcs = 0
+    const ctx = {
+      font: '12px sans-serif',
+      beginPath() {},
+      stroke() {},
+      fill() {},
+      resetTransform() {},
+      scale() {},
+      translate() {},
+      moveTo() {},
+      lineTo() {},
+      arc() {
+        arcs++
+      },
+    } as unknown as RenderCtx
+
+    const clickMap = new ClickMapIndex()
+    renderTreeCanvas({
+      model,
+      ctx,
+      clickMap,
+      offsetY: 0,
+      theme: { palette: { text: { primary: '#000' } } } as Theme,
+    })
+    return { arcs, hits: clickMap.search(bounds) }
+  }
+
+  it('indexes the internal nodes when the bubbles are drawn', () => {
+    const { arcs, hits } = renderWithBubbles(true)
+    expect(arcs).toBe(3)
+    expect(hits.filter(h => h.branch).length).toBe(3)
+  })
+
+  it('indexes them just the same when the bubbles are off', () => {
+    const { arcs, hits } = renderWithBubbles(false)
+    expect(arcs).toBe(0)
+    expect(hits.filter(h => h.branch).length).toBe(3)
+  })
+})

package/src/components/tree/renderTreeCanvas.ts

@@ -171,6 +171,8 @@ function renderCollapsedTriangles({
   })
 }
 
+// the bubbles are click targets whether or not they are painted, so this pass
+// always runs and `draw` only decides whether it also strokes the circles
 function renderNodeBubbles({
   ctx,
   clickMap,
@@ -180,6 +182,7 @@ function renderNodeBubbles({
   maxDepthToLeaf,
   blockSizeYOverride,
   collapsedSet,
+  draw,
 }: {
   ctx: RenderCtx
   clickMap?: ClickMapIndex
@@ -189,6 +192,7 @@ function renderNodeBubbles({
   maxDepthToLeaf: number
   blockSizeYOverride?: number
   collapsedSet: Set<string>
+  draw: boolean
 }) {
   const {
     hierarchy,
@@ -207,12 +211,14 @@ function renderNodeBubbles({
     const { id, name } = data
     if (node.height >= 1 && inYBlock(y, offsetY, by)) {
       const isCollapsed = collapsedSet.has(id)
-      ctx.strokeStyle = 'black'
-      ctx.fillStyle = isCollapsed ? 'black' : 'white'
-      ctx.beginPath()
-      ctx.arc(x, y, radius, 0, 2 * Math.PI)
-      ctx.fill()
-      ctx.stroke()
+      if (draw) {
+        ctx.strokeStyle = 'black'
+        ctx.fillStyle = isCollapsed ? 'black' : 'white'
+        ctx.beginPath()
+        ctx.arc(x, y, radius, 0, 2 * Math.PI)
+        ctx.fill()
+        ctx.stroke()
+      }
 
       // collapsed nodes get their click/hover target from the triangle pass,
       // which covers the apex bubble and carries a descriptive label
@@ -417,18 +423,17 @@ export function renderTreeCanvas({
       collapsedSet,
     })
 
-    if (drawNodeBubbles) {
-      renderNodeBubbles({
-        ctx,
-        offsetY,
-        clickMap,
-        model,
-        tipX,
-        maxDepthToLeaf,
-        blockSizeYOverride,
-        collapsedSet,
-      })
-    }
+    renderNodeBubbles({
+      ctx,
+      offsetY,
+      clickMap,
+      model,
+      tipX,
+      maxDepthToLeaf,
+      blockSizeYOverride,
+      collapsedSet,
+      draw: drawNodeBubbles,
+    })
   }
 
   if (showTreeText) {

package/src/model/treeModel.ts

@@ -56,7 +56,7 @@ export function TreeModelF() {
 
       /**
        * #property
-       * draw clickable node bubbles on the tree
+       * draw node bubbles on the tree; the branches stay clickable either way
        */
       drawNodeBubbles: stripDefault(types.boolean, defaultDrawNodeBubbles),
 

package/src/version.ts

@@ -1 +1 @@
-export const version = '6.1.0'
+export const version = '6.1.1'