Hide leaf nodes

GMOD · Feb 27, 2024 · 192868a · 192868a
1 parent cc4056c
commit 192868a
Show file tree

Hide file tree

Showing 4 changed files with 47 additions and 46 deletions.
diff --git a/lib/src/components/TreePanel/TreeNodeMenu.tsx b/lib/src/components/TreePanel/TreeNodeMenu.tsx
@@ -17,7 +17,7 @@ const TreeMenu = observer(function ({
   model: MsaViewModel
   onClose: () => void
 }) {
-  const { selectedStructures, collapsed, structures } = model
+  const { selectedStructures, collapsed, collapsed2, structures } = model
   const nodeDetails = node ? model.getRowData(node.name) : undefined
 
   return (
@@ -56,11 +56,21 @@ const TreeMenu = observer(function ({
       <MenuItem
         dense
         onClick={() => {
-          model.toggleCollapsed(node.id)
+          if (collapsed.includes(node.id)) {
+            model.toggleCollapsed(node.id)
+          } else {
+            if (node.id.endsWith('-leafnode')) {
+              model.toggleCollapsed2(`${node.id}`)
+            } else {
+              model.toggleCollapsed2(`${node.id}-leafnode`)
+            }
+          }
           onClose()
         }}
       >
-        {collapsed.includes(node.id) ? 'Show node' : 'Hide node'}
+        {collapsed.includes(node.id) || collapsed2.includes(node.id)
+          ? 'Show node'
+          : 'Hide node'}
       </MenuItem>
 
       {structures[node.name]?.map(entry =>

diff --git a/lib/src/components/TreePanel/renderTreeCanvas.ts b/lib/src/components/TreePanel/renderTreeCanvas.ts
@@ -90,6 +90,7 @@ export function renderNodeBubbles({
     } = node
     const { branchset, id = '', name = '' } = data
     if (
+      !id.endsWith('-leafnode') &&
       branchset.length &&
       y > offsetY - extendBounds &&
       y < offsetY + by + extendBounds

diff --git a/lib/src/model.ts b/lib/src/model.ts
@@ -18,7 +18,6 @@ import BaseViewModel from '@jbrowse/core/pluggableElementTypes/models/BaseViewMo
 import {
   clamp,
   collapse,
-  filterHiddenLeafNodes,
   generateNodeIds,
   maxLength,
   setBrLength,
@@ -92,6 +91,21 @@ export type BasicTrack = IBoxTrack | ITextTrack
  */
 function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
 
+function reparseTree(tree: NodeWithIds): NodeWithIds {
+  return {
+    ...tree,
+    branchset: tree.branchset.map(r =>
+      r.branchset.length
+        ? reparseTree(r)
+        : {
+            branchset: [r],
+            id: `${r.id}-leafnode`,
+            name: `${r.name}-hidden`,
+          },
+    ),
+  }
+}
+
 export type DialogComponentType =
   // eslint-disable-next-line @typescript-eslint/no-explicit-any
   | React.LazyExoticComponent<React.FC<any>>
@@ -239,12 +253,7 @@ const model = types
        */
       collapsed: types.array(types.string),
 
-      /**
-       * #property
-       * array of leaf nodes that are 'hidden', similar to collapsed but for leaf nodes
-       */
-      hidden: types.array(types.string),
-
+      collapsed2: types.array(types.string),
       /**
        * #property
        * focus on particular subtree
@@ -426,20 +435,6 @@ const model = types
       self.drawTree = arg
     },
 
-    /**
-     * #action
-     */
-    hideNode(arg: string) {
-      self.hidden.push(arg)
-    },
-
-    /**
-     * #action
-     */
-    clearHidden() {
-      self.hidden.clear()
-    },
-
     /**
      * #action
      */
@@ -451,6 +446,16 @@ const model = types
       }
     },
 
+    /**
+     * #action
+     */
+    toggleCollapsed2(node: string) {
+      if (self.collapsed2.includes(node)) {
+        self.collapsed2.remove(node)
+      } else {
+        self.collapsed2.push(node)
+      }
+    },
     /**
      * #action
      */
@@ -613,14 +618,15 @@ const model = types
      * #getter
      */
     get _tree(): NodeWithIds {
-      return self.data.tree
+      const ret = self.data.tree
         ? generateNodeIds(parseNewick(self.data.tree))
         : this.MSA?.getTree() || {
             noTree: true,
             branchset: [],
             id: 'empty',
             name: 'empty',
           }
+      return reparseTree(ret)
     },
     /**
      * #getter
@@ -659,18 +665,13 @@ const model = types
         }
       }
 
-      if (self.collapsed.length) {
-        self.collapsed
+      if (self.collapsed.length || self.collapsed2.length) {
+        ;[...self.collapsed, ...self.collapsed2]
           .map(collapsedId => hier.find(node => node.data.id === collapsedId))
           .filter(notEmpty)
           .map(node => collapse(node))
       }
-      if (self.hidden.length) {
-        self.hidden
-          .map(hiddenId => hier.find(node => node.data.id === hiddenId))
-          .filter(notEmpty)
-          .map(node => filterHiddenLeafNodes(node.parent, node.id))
-      }
+
       return hier
     },
     /**
@@ -1093,7 +1094,7 @@ const model = types
     relativePxToBp(rowName: string, position: number) {
       const { rowNames, rows } = self
       const index = rowNames.indexOf(rowName)
-      if (index !== -1) {
+      if (index !== -1 && rows[index]) {
         const row = rows[index][1]
 
         let k = 0
@@ -1115,7 +1116,7 @@ const model = types
     relativePxToBp2(rowName: string, position: number) {
       const { rowNames, rows } = self
       const index = rowNames.indexOf(rowName)
-      if (index !== -1) {
+      if (index !== -1 && rows[index]) {
         const row = rows[index][1]
 
         let k = 0

diff --git a/lib/src/util.ts b/lib/src/util.ts
@@ -145,17 +145,6 @@ export function collapse(d: HierarchyNode<NodeWithIds>) {
   }
 }
 
-// Collapse the node and all it's children, from
-// https://bl.ocks.org/d3noob/43a860bc0024792f8803bba8ca0d5ecd
-export function filterHiddenLeafNodes(
-  d: HierarchyNode<NodeWithIds> | null,
-  hiddenId?: string,
-) {
-  if (d?.children) {
-    d.children = d.children.filter(f => f.id !== hiddenId)
-  }
-}
-
 export function clamp(min: number, num: number, max: number) {
   return Math.min(Math.max(num, min), max)
 }