react-msaview 3.2.1 → 4.0.0

package/src/model.ts

@@ -42,6 +42,7 @@ import TextTrack from './components/TextTrack'
 
 // parsers
 import ClustalMSA from './parsers/ClustalMSA'
+import EmfMSA from './parsers/EmfMSA'
 import StockholmMSA from './parsers/StockholmMSA'
 import FastaMSA from './parsers/FastaMSA'
 import parseNewick from './parseNewick'
@@ -57,6 +58,7 @@ import {
   mouseOverCoordToGlobalCoord,
   globalCoordToRowSpecificCoord,
 } from './rowCoordinateCalculations'
+import EmfTree from './parsers/EmfTree'
 
 export interface Accession {
   accession: string
@@ -150,7 +152,7 @@ function stateModelFactory() {
          * #property
          * height of each row, px
          */
-        rowHeight: 20,
+        rowHeight: 18,
 
         /**
          * #property
@@ -168,7 +170,7 @@ function stateModelFactory() {
          * #property
          * width of columns, px
          */
-        colWidth: 16,
+        colWidth: 14,
 
         /**
          * #property
@@ -224,7 +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
@@ -476,7 +482,7 @@ function stateModelFactory() {
       /**
        * #action
        */
-      setData(data: { msa?: string; tree?: string }) {
+      setData(data: { msa?: string; tree?: string; treeMetadata?: string }) {
         self.data = cast(data)
       },
 
@@ -614,11 +620,13 @@ function stateModelFactory() {
         if (text) {
           if (Stockholm.sniff(text)) {
             return new StockholmMSA(text, self.currentAlignment)
-          }
-          if (text.startsWith('>')) {
+          } else if (text.startsWith('>')) {
             return new FastaMSA(text)
+          } else if (text.startsWith('SEQ')) {
+            return new EmfMSA(text)
+          } else {
+            return new ClustalMSA(text)
           }
-          return new ClustalMSA(text)
         }
         return null
       },
@@ -633,14 +641,25 @@ function stateModelFactory() {
        * #getter
        */
       get tree(): NodeWithIds {
-        const ret = self.data.tree
-          ? generateNodeIds(parseNewick(self.data.tree))
-          : this.MSA?.getTree() || {
-              noTree: true,
-              branchset: [],
-              id: 'empty',
-              name: 'empty',
-            }
+        const text = self.data.tree
+        let ret: NodeWithIds
+        if (text) {
+          let t: string
+          if (text.startsWith('SEQ')) {
+            const r = new EmfTree(text)
+            t = r.data.tree
+          } else {
+            t = text
+          }
+          ret = generateNodeIds(parseNewick(t))
+        } else {
+          ret = this.MSA?.getTree() || {
+            noTree: true,
+            children: [],
+            id: 'empty',
+            name: 'empty',
+          }
+        }
         return reparseTree(ret)
       },
       /**
@@ -661,10 +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) {
@@ -766,7 +785,7 @@ function stateModelFactory() {
        * #getter
        */
       get fontSize() {
-        return Math.min(Math.max(6, self.rowHeight - 8), 18)
+        return Math.min(Math.max(6, self.rowHeight - 3), 18)
       },
       /**
        * #getter

package/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

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 = '4.0.0'