react-msaview 3.2.1 → 3.2.2

package/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: [],
       })),
     }
   }

package/src/parsers/EmfMSA.ts

@@ -0,0 +1,66 @@
+import { parseEmfAln } from 'emf-js'
+import type { NodeWithIds } from '../util'
+
+export default class EmfMSA {
+  private MSA: ReturnType<typeof parseEmfAln>
+
+  constructor(text: string) {
+    this.MSA = parseEmfAln(text)
+  }
+
+  getMSA() {
+    return this.MSA
+  }
+
+  getRow(name: string): string {
+    return this.MSA.find(aln => aln.protein === name)?.seq || ''
+  }
+
+  getWidth() {
+    return this.MSA[0]!.seq.length
+  }
+
+  getRowData() {
+    return undefined
+  }
+
+  getHeader() {
+    return ''
+  }
+
+  getNames() {
+    return this.MSA.map(aln => aln.protein)
+  }
+
+  getStructures() {
+    return {}
+  }
+
+  get alignmentNames() {
+    return []
+  }
+
+  getTree(): NodeWithIds {
+    return {
+      id: 'root',
+      name: 'root',
+      noTree: true,
+      children: this.getNames().map(name => ({
+        id: name,
+        name,
+        children: [],
+      })),
+    }
+  }
+
+  get seqConsensus() {
+    return undefined
+  }
+  get secondaryStructureConsensus() {
+    return undefined
+  }
+
+  get tracks() {
+    return []
+  }
+}

package/src/parsers/EmfTree.ts

@@ -0,0 +1,9 @@
+import { parseEmfTree } from 'emf-js'
+
+export default class EmfTree {
+  data: ReturnType<typeof parseEmfTree>
+
+  constructor(text: string) {
+    this.data = parseEmfTree(text)
+  }
+}

package/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,
       })),
     }

package/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,
           })),
         }

package/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`,
           },

package/src/util.ts

@@ -14,7 +14,7 @@ export function transform<T>(
 }
 
 interface Node {
-  branchset?: Node[]
+  children?: Node[]
   name?: string
   [key: string]: unknown
 }
@@ -22,7 +22,7 @@ interface Node {
 export interface NodeWithIds {
   id: string
   name: string
-  branchset: NodeWithIds[]
+  children: NodeWithIds[]
   length?: number
   noTree?: boolean
 }
@@ -30,7 +30,7 @@ export interface NodeWithIds {
 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),
       ) || [],
   }

package/src/version.ts

@@ -1 +1 @@
-export const version = '3.2.1'
+export const version = '3.2.2'