Rename branchset to children

app/src/App.tsx

@@ -22,7 +22,7 @@ const mymodel = AppGlobal.create(
       },
 )
 
-let lastTime = 0
+const lastTime = 0
 // onSnapshot(mymodel, snap => {
 //   const now = Date.now()
 //   if (now - lastTime >= 1000) {

lib/src/model.ts

@@ -226,7 +226,11 @@ function stateModelFactory() {
          * data from the loaded tree/msa/treeMetadata, generally loaded by
          * autorun
          */
-        data: types.optional(DataModelF(), { tree: '', msa: '' }),
+        data: types.optional(DataModelF(), {
+          tree: '',
+          msa: '',
+          treeMetadata: '',
+        }),
 
         /**
          * #property
@@ -478,7 +482,7 @@ function stateModelFactory() {
       /**
        * #action
        */
-      setData(data: { msa?: string; tree?: string }) {
+      setData(data: { msa?: string; tree?: string; treeMetadata?: string }) {
         self.data = cast(data)
       },
 
@@ -651,7 +655,7 @@ function stateModelFactory() {
         } else {
           ret = this.MSA?.getTree() || {
             noTree: true,
-            branchset: [],
+            children: [],
             id: 'empty',
             name: 'empty',
           }
@@ -676,10 +680,10 @@ function stateModelFactory() {
        * #getter
        */
       get root() {
-        let hier = hierarchy(this.tree, d => d.branchset)
-          // todo: investigate whether needed, typescript says branchset always true
+        let hier = hierarchy(this.tree, d => d.children)
+          // todo: investigate whether needed, typescript says children always true
           // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
-          .sum(d => (d.branchset ? 0 : 1))
+          .sum(d => (d.children ? 0 : 1))
           .sort((a, b) => ascending(a.data.length || 1, b.data.length || 1))
 
         if (self.showOnly) {

lib/src/parseNewick.ts

@@ -34,13 +34,13 @@
  * Converted to JSON:
  * {
  *   name: "F",
- *   branchset: [
+ *   children: [
  *     {name: "A", length: 0.1},
  *     {name: "B", length: 0.2},
  *     {
  *       name: "E",
  *       length: 0.5,
- *       branchset: [
+ *       children: [
  *         {name: "C", length: 0.3},
  *         {name: "D", length: 0.4}
  *       ]
@@ -50,9 +50,9 @@
  *
  * Converted to JSON, but with no names or lengths:
  * {
- *   branchset: [
+ *   children: [
  *     {}, {}, {
- *       branchset: [{}, {}]
+ *       children: [{}, {}]
  *     }
  *   ]
  * }
@@ -66,13 +66,13 @@ export default function parse(s: string) {
     const token = tokens[i]!
     const subtree = {}
     switch (token) {
-      case '(': // new branchset
-        tree.branchset = [subtree]
+      case '(': // new children
+        tree.children = [subtree]
         ancestors.push(tree)
         tree = subtree
         break
       case ',': // another branch
-        ancestors.at(-1)?.branchset.push(subtree)
+        ancestors.at(-1)?.children.push(subtree)
         tree = subtree
         break
       case ')': // optional name next

lib/src/parsers/ClustalMSA.ts

@@ -44,10 +44,10 @@ export default class ClustalMSA {
       id: 'root',
       name: 'root',
       noTree: true,
-      branchset: this.getNames().map(name => ({
+      children: this.getNames().map(name => ({
         id: name,
         name,
-        branchset: [],
+        children: [],
       })),
     }
   }

lib/src/parsers/EmfMSA.ts

@@ -45,10 +45,10 @@ export default class EmfMSA {
       id: 'root',
       name: 'root',
       noTree: true,
-      branchset: this.getNames().map(name => ({
+      children: this.getNames().map(name => ({
         id: name,
         name,
-        branchset: [],
+        children: [],
       })),
     }
   }

lib/src/parsers/FastaMSA.ts

@@ -61,9 +61,9 @@ export default class FastaMSA {
       id: 'root',
       name: 'root',
       noTree: true,
-      branchset: this.getNames().map(name => ({
+      children: this.getNames().map(name => ({
         id: name,
-        branchset: [],
+        children: [],
         name,
       })),
     }

lib/src/parsers/StockholmMSA.ts

@@ -100,9 +100,9 @@ export default class StockholmMSA {
           id: 'root',
           name: 'root',
           noTree: true,
-          branchset: this.getNames().map(name => ({
+          children: this.getNames().map(name => ({
             id: name,
-            branchset: [],
+            children: [],
             name,
           })),
         }

lib/src/reparseTree.ts

@@ -3,11 +3,11 @@ import type { NodeWithIds } from './util'
 export function reparseTree(tree: NodeWithIds): NodeWithIds {
   return {
     ...tree,
-    branchset: tree.branchset.map(r =>
-      r.branchset.length
+    children: tree.children.map(r =>
+      r.children.length
         ? reparseTree(r)
         : {
-            branchset: [r],
+            children: [r],
             id: `${r.id}-leafnode`,
             name: `${r.name}-hidden`,
           },

lib/src/util.ts

@@ -14,23 +14,23 @@ export function transform<T>(
 }
 
 interface Node {
-  branchset?: Node[]
+  children?: Node[]
   name?: string
   [key: string]: unknown
 }
 
 export interface NodeWithIds {
   id: string
   name: string
-  branchset: NodeWithIds[]
+  children: NodeWithIds[]
   length?: number
   noTree?: boolean
 }
 
 export interface NodeWithIdsAndLength {
   id: string
   name: string
-  branchset: NodeWithIdsAndLength[]
+  children: NodeWithIdsAndLength[]
   noTree?: boolean
   length: number
 }
@@ -46,8 +46,8 @@ export function generateNodeIds(
     ...tree,
     id,
     name: tree.name || id,
-    branchset:
-      tree.branchset?.map((b, i) =>
+    children:
+      tree.children?.map((b, i) =>
         generateNodeIds(b, `${id}-${i}`, depth + 1),
       ) || [],
   }