react-msaview 3.2.1 → 3.2.2

package/dist/parseNewick.js.map

@@ -1 +1 @@
-{"version":3,"file":"parseNewick.js","sourceRoot":"","sources":["../src/parseNewick.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA0DG;AACH,MAAM,CAAC,OAAO,UAAU,KAAK,CAAC,CAAS;IACrC,MAAM,SAAS,GAAG,EAAE,CAAA;IAEpB,IAAI,IAAI,GAAG,EAAyB,CAAA;IACpC,MAAM,MAAM,GAAG,CAAC,CAAC,KAAK,CAAC,qBAAqB,CAAC,CAAA;IAC7C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QACvC,MAAM,KAAK,GAAG,MAAM,CAAC,CAAC,CAAE,CAAA;QACxB,MAAM,OAAO,GAAG,EAAE,CAAA;QAClB,QAAQ,KAAK,EAAE,CAAC;YACd,KAAK,GAAG,EAAE,gBAAgB;gBACxB,IAAI,CAAC,SAAS,GAAG,CAAC,OAAO,CAAC,CAAA;gBAC1B,SAAS,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;gBACpB,IAAI,GAAG,OAAO,CAAA;gBACd,MAAK;YACP,KAAK,GAAG,EAAE,iBAAiB;gBACzB,SAAS,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,EAAE,SAAS,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;gBACzC,IAAI,GAAG,OAAO,CAAA;gBACd,MAAK;YACP,KAAK,GAAG,EAAE,qBAAqB;gBAC7B,IAAI,GAAG,SAAS,CAAC,GAAG,EAAG,CAAA;gBACvB,MAAK;YACP,KAAK,GAAG,EAAE,uBAAuB;gBAC/B,MAAK;YACP,OAAO,CAAC,CAAC,CAAC;gBACR,MAAM,CAAC,GAAG,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,CAAA;gBACxB,IAAI,CAAC,KAAK,GAAG,IAAI,CAAC,KAAK,GAAG,IAAI,CAAC,KAAK,GAAG,EAAE,CAAC;oBACxC,IAAI,CAAC,IAAI,GAAG,KAAK,CAAA;gBACnB,CAAC;qBAAM,IAAI,CAAC,KAAK,GAAG,EAAE,CAAC;oBACrB,IAAI,CAAC,MAAM,GAAG,MAAM,CAAC,UAAU,CAAC,KAAK,CAAC,CAAA;gBACxC,CAAC;YACH,CAAC;QACH,CAAC;IACH,CAAC;IACD,OAAO,IAAI,CAAA;AACb,CAAC"}
+{"version":3,"file":"parseNewick.js","sourceRoot":"","sources":["../src/parseNewick.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA0DG;AACH,MAAM,CAAC,OAAO,UAAU,KAAK,CAAC,CAAS;IACrC,MAAM,SAAS,GAAG,EAAE,CAAA;IAEpB,IAAI,IAAI,GAAG,EAAyB,CAAA;IACpC,MAAM,MAAM,GAAG,CAAC,CAAC,KAAK,CAAC,qBAAqB,CAAC,CAAA;IAC7C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QACvC,MAAM,KAAK,GAAG,MAAM,CAAC,CAAC,CAAE,CAAA;QACxB,MAAM,OAAO,GAAG,EAAE,CAAA;QAClB,QAAQ,KAAK,EAAE,CAAC;YACd,KAAK,GAAG,EAAE,eAAe;gBACvB,IAAI,CAAC,QAAQ,GAAG,CAAC,OAAO,CAAC,CAAA;gBACzB,SAAS,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;gBACpB,IAAI,GAAG,OAAO,CAAA;gBACd,MAAK;YACP,KAAK,GAAG,EAAE,iBAAiB;gBACzB,SAAS,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,EAAE,QAAQ,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;gBACxC,IAAI,GAAG,OAAO,CAAA;gBACd,MAAK;YACP,KAAK,GAAG,EAAE,qBAAqB;gBAC7B,IAAI,GAAG,SAAS,CAAC,GAAG,EAAG,CAAA;gBACvB,MAAK;YACP,KAAK,GAAG,EAAE,uBAAuB;gBAC/B,MAAK;YACP,OAAO,CAAC,CAAC,CAAC;gBACR,MAAM,CAAC,GAAG,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,CAAA;gBACxB,IAAI,CAAC,KAAK,GAAG,IAAI,CAAC,KAAK,GAAG,IAAI,CAAC,KAAK,GAAG,EAAE,CAAC;oBACxC,IAAI,CAAC,IAAI,GAAG,KAAK,CAAA;gBACnB,CAAC;qBAAM,IAAI,CAAC,KAAK,GAAG,EAAE,CAAC;oBACrB,IAAI,CAAC,MAAM,GAAG,MAAM,CAAC,UAAU,CAAC,KAAK,CAAC,CAAA;gBACxC,CAAC;YACH,CAAC;QACH,CAAC;IACH,CAAC;IACD,OAAO,IAAI,CAAA;AACb,CAAC"}

package/dist/parsers/ClustalMSA.d.ts

@@ -5,8 +5,8 @@ export default class ClustalMSA {
     getMSA(): {
         consensus: string;
         alns: {
-            id: any;
-            seq: any;
+            id: string;
+            seq: string;
         }[];
         header: {
             info: string;
@@ -14,13 +14,13 @@ export default class ClustalMSA {
         };
     };
     getRow(name: string): string;
-    getWidth(): any;
+    getWidth(): number;
     getRowData(): undefined;
     getHeader(): {
         info: string;
         version: string;
     };
-    getNames(): any[];
+    getNames(): string[];
     getStructures(): {};
     get alignmentNames(): never[];
     getTree(): NodeWithIds;

package/dist/parsers/ClustalMSA.js

@@ -33,10 +33,10 @@ 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/dist/parsers/ClustalMSA.js.map

@@ -1 +1 @@
-{"version":3,"file":"ClustalMSA.js","sourceRoot":"","sources":["../../src/parsers/ClustalMSA.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,YAAY,CAAA;AAElC,MAAM,CAAC,OAAO,OAAO,UAAU;IACrB,GAAG,CAA0B;IAErC,YAAY,IAAY;QACtB,IAAI,CAAC,GAAG,GAAG,KAAK,CAAC,IAAI,CAAC,CAAA;IACxB,CAAC;IAED,MAAM;QACJ,OAAO,IAAI,CAAC,GAAG,CAAA;IACjB,CAAC;IAED,MAAM,CAAC,IAAY;QACjB,OAAO,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,KAAK,IAAI,CAAC,EAAE,GAAG,IAAI,EAAE,CAAA;IAC9D,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,CAAE,CAAC,GAAG,CAAC,MAAM,CAAA;IACrC,CAAC;IAED,UAAU;QACR,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,SAAS;QACP,OAAO,IAAI,CAAC,GAAG,CAAC,MAAM,CAAA;IACxB,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,CAAA;IACzC,CAAC;IAED,aAAa;QACX,OAAO,EAAE,CAAA;IACX,CAAC;IAED,IAAI,cAAc;QAChB,OAAO,EAAE,CAAA;IACX,CAAC;IAED,OAAO;QACL,OAAO;YACL,EAAE,EAAE,MAAM;YACV,IAAI,EAAE,MAAM;YACZ,MAAM,EAAE,IAAI;YACZ,SAAS,EAAE,IAAI,CAAC,QAAQ,EAAE,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;gBACtC,EAAE,EAAE,IAAI;gBACR,IAAI;gBACJ,SAAS,EAAE,EAAE;aACd,CAAC,CAAC;SACJ,CAAA;IACH,CAAC;IAED,IAAI,YAAY;QACd,OAAO,IAAI,CAAC,GAAG,CAAC,SAAS,CAAA;IAC3B,CAAC;IACD,IAAI,2BAA2B;QAC7B,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,IAAI,MAAM;QACR,OAAO,EAAE,CAAA;IACX,CAAC;CACF"}
+{"version":3,"file":"ClustalMSA.js","sourceRoot":"","sources":["../../src/parsers/ClustalMSA.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,YAAY,CAAA;AAElC,MAAM,CAAC,OAAO,OAAO,UAAU;IACrB,GAAG,CAA0B;IAErC,YAAY,IAAY;QACtB,IAAI,CAAC,GAAG,GAAG,KAAK,CAAC,IAAI,CAAC,CAAA;IACxB,CAAC;IAED,MAAM;QACJ,OAAO,IAAI,CAAC,GAAG,CAAA;IACjB,CAAC;IAED,MAAM,CAAC,IAAY;QACjB,OAAO,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,KAAK,IAAI,CAAC,EAAE,GAAG,IAAI,EAAE,CAAA;IAC9D,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,CAAE,CAAC,GAAG,CAAC,MAAM,CAAA;IACrC,CAAC;IAED,UAAU;QACR,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,SAAS;QACP,OAAO,IAAI,CAAC,GAAG,CAAC,MAAM,CAAA;IACxB,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,CAAA;IACzC,CAAC;IAED,aAAa;QACX,OAAO,EAAE,CAAA;IACX,CAAC;IAED,IAAI,cAAc;QAChB,OAAO,EAAE,CAAA;IACX,CAAC;IAED,OAAO;QACL,OAAO;YACL,EAAE,EAAE,MAAM;YACV,IAAI,EAAE,MAAM;YACZ,MAAM,EAAE,IAAI;YACZ,QAAQ,EAAE,IAAI,CAAC,QAAQ,EAAE,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;gBACrC,EAAE,EAAE,IAAI;gBACR,IAAI;gBACJ,QAAQ,EAAE,EAAE;aACb,CAAC,CAAC;SACJ,CAAA;IACH,CAAC;IAED,IAAI,YAAY;QACd,OAAO,IAAI,CAAC,GAAG,CAAC,SAAS,CAAA;IAC3B,CAAC;IACD,IAAI,2BAA2B;QAC7B,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,IAAI,MAAM;QACR,OAAO,EAAE,CAAA;IACX,CAAC;CACF"}

package/dist/parsers/EmfMSA.d.ts

@@ -0,0 +1,27 @@
+import type { NodeWithIds } from '../util';
+export default class EmfMSA {
+    private MSA;
+    constructor(text: string);
+    getMSA(): {
+        species: string;
+        protein: string;
+        chr: string;
+        start: number;
+        end: number;
+        strand: number;
+        geneId: string;
+        unknown: string;
+        seq: string;
+    }[];
+    getRow(name: string): string;
+    getWidth(): number;
+    getRowData(): undefined;
+    getHeader(): string;
+    getNames(): string[];
+    getStructures(): {};
+    get alignmentNames(): never[];
+    getTree(): NodeWithIds;
+    get seqConsensus(): undefined;
+    get secondaryStructureConsensus(): undefined;
+    get tracks(): never[];
+}

package/dist/parsers/EmfMSA.js

@@ -0,0 +1,53 @@
+import { parseEmfAln } from 'emf-js';
+export default class EmfMSA {
+    MSA;
+    constructor(text) {
+        this.MSA = parseEmfAln(text);
+    }
+    getMSA() {
+        return this.MSA;
+    }
+    getRow(name) {
+        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() {
+        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 [];
+    }
+}
+//# sourceMappingURL=EmfMSA.js.map

package/dist/parsers/EmfMSA.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"EmfMSA.js","sourceRoot":"","sources":["../../src/parsers/EmfMSA.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAE,MAAM,QAAQ,CAAA;AAGpC,MAAM,CAAC,OAAO,OAAO,MAAM;IACjB,GAAG,CAAgC;IAE3C,YAAY,IAAY;QACtB,IAAI,CAAC,GAAG,GAAG,WAAW,CAAC,IAAI,CAAC,CAAA;IAC9B,CAAC;IAED,MAAM;QACJ,OAAO,IAAI,CAAC,GAAG,CAAA;IACjB,CAAC;IAED,MAAM,CAAC,IAAY;QACjB,OAAO,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,OAAO,KAAK,IAAI,CAAC,EAAE,GAAG,IAAI,EAAE,CAAA;IAC9D,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,GAAG,CAAC,CAAC,CAAE,CAAC,GAAG,CAAC,MAAM,CAAA;IAChC,CAAC;IAED,UAAU;QACR,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,SAAS;QACP,OAAO,EAAE,CAAA;IACX,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;IACzC,CAAC;IAED,aAAa;QACX,OAAO,EAAE,CAAA;IACX,CAAC;IAED,IAAI,cAAc;QAChB,OAAO,EAAE,CAAA;IACX,CAAC;IAED,OAAO;QACL,OAAO;YACL,EAAE,EAAE,MAAM;YACV,IAAI,EAAE,MAAM;YACZ,MAAM,EAAE,IAAI;YACZ,QAAQ,EAAE,IAAI,CAAC,QAAQ,EAAE,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;gBACrC,EAAE,EAAE,IAAI;gBACR,IAAI;gBACJ,QAAQ,EAAE,EAAE;aACb,CAAC,CAAC;SACJ,CAAA;IACH,CAAC;IAED,IAAI,YAAY;QACd,OAAO,SAAS,CAAA;IAClB,CAAC;IACD,IAAI,2BAA2B;QAC7B,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,IAAI,MAAM;QACR,OAAO,EAAE,CAAA;IACX,CAAC;CACF"}

package/dist/parsers/EmfTree.d.ts

@@ -0,0 +1,5 @@
+import { parseEmfTree } from 'emf-js';
+export default class EmfTree {
+    data: ReturnType<typeof parseEmfTree>;
+    constructor(text: string);
+}

package/dist/parsers/EmfTree.js

@@ -0,0 +1,8 @@
+import { parseEmfTree } from 'emf-js';
+export default class EmfTree {
+    data;
+    constructor(text) {
+        this.data = parseEmfTree(text);
+    }
+}
+//# sourceMappingURL=EmfTree.js.map

package/dist/parsers/EmfTree.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"EmfTree.js","sourceRoot":"","sources":["../../src/parsers/EmfTree.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,YAAY,EAAE,MAAM,QAAQ,CAAA;AAErC,MAAM,CAAC,OAAO,OAAO,OAAO;IAC1B,IAAI,CAAiC;IAErC,YAAY,IAAY;QACtB,IAAI,CAAC,IAAI,GAAG,YAAY,CAAC,IAAI,CAAC,CAAA;IAChC,CAAC;CACF"}

package/dist/parsers/FastaMSA.js

@@ -48,9 +48,9 @@ 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/dist/parsers/FastaMSA.js.map

@@ -1 +1 @@
-{"version":3,"file":"FastaMSA.js","sourceRoot":"","sources":["../../src/parsers/FastaMSA.ts"],"names":[],"mappings":"AAEA,SAAS,eAAe,CAAC,IAAY;IACnC,OAAO,IAAI;SACR,KAAK,CAAC,GAAG,CAAC;SACV,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;SACzB,GAAG,CAAC,SAAS,CAAC,EAAE;QACf,MAAM,CAAC,OAAO,EAAE,GAAG,QAAQ,CAAC,GAAG,SAAS,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACpD,MAAM,CAAC,EAAE,EAAE,GAAG,WAAW,CAAC,GAAG,OAAQ,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;QAChD,MAAM,cAAc,GAAG,WAAW,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;QAC5C,MAAM,WAAW,GAAG,QAAQ,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;QACrC,MAAM,QAAQ,GAAG,WAAW,CAAC,UAAU,CAAC,KAAK,EAAE,EAAE,CAAC,CAAA;QAClD,OAAO,EAAE,EAAE,EAAE,WAAW,EAAE,cAAc,EAAE,QAAQ,EAAE,CAAA;IACtD,CAAC,CAAC,CAAA;AACN,CAAC;AACD,MAAM,CAAC,OAAO,OAAO,QAAQ;IACnB,GAAG,CAAqC;IAChD,YAAY,IAAY;QACtB,IAAI,CAAC,GAAG,GAAG;YACT,OAAO,EAAE,MAAM,CAAC,WAAW,CACzB,eAAe,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,QAAQ,CAAC,CAAC,CACnD;SACF,CAAA;IACH,CAAC;IAED,MAAM;QACJ,OAAO,IAAI,CAAC,GAAG,CAAA;IACjB,CAAC;IAED,UAAU;QACR,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,QAAQ;QACN,OAAO,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;IACtC,CAAC;IAED,MAAM,CAAC,IAAY;QACjB,OAAO,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,IAAI,CAAC,IAAI,EAAE,CAAA;IACrC,CAAC;IAED,QAAQ;QACN,MAAM,IAAI,GAAG,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,CAAE,CAAA;QAC9C,OAAO,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,MAAM,CAAA;IACjC,CAAC;IAED,aAAa;QACX,OAAO,EAAE,CAAA;IACX,CAAC;IAED,IAAI,cAAc;QAChB,OAAO,EAAE,CAAA;IACX,CAAC;IAED,SAAS;QACP,OAAO,EAAE,CAAA;IACX,CAAC;IAED,OAAO;QACL,OAAO;YACL,EAAE,EAAE,MAAM;YACV,IAAI,EAAE,MAAM;YACZ,MAAM,EAAE,IAAI;YACZ,SAAS,EAAE,IAAI,CAAC,QAAQ,EAAE,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;gBACtC,EAAE,EAAE,IAAI;gBACR,SAAS,EAAE,EAAE;gBACb,IAAI;aACL,CAAC,CAAC;SACJ,CAAA;IACH,CAAC;IAED,IAAI,YAAY;QACd,OAAO,SAAS,CAAA;IAClB,CAAC;IACD,IAAI,2BAA2B;QAC7B,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,IAAI,MAAM;QACR,OAAO,EAAE,CAAA;IACX,CAAC;CACF"}
+{"version":3,"file":"FastaMSA.js","sourceRoot":"","sources":["../../src/parsers/FastaMSA.ts"],"names":[],"mappings":"AAEA,SAAS,eAAe,CAAC,IAAY;IACnC,OAAO,IAAI;SACR,KAAK,CAAC,GAAG,CAAC;SACV,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;SACzB,GAAG,CAAC,SAAS,CAAC,EAAE;QACf,MAAM,CAAC,OAAO,EAAE,GAAG,QAAQ,CAAC,GAAG,SAAS,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACpD,MAAM,CAAC,EAAE,EAAE,GAAG,WAAW,CAAC,GAAG,OAAQ,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;QAChD,MAAM,cAAc,GAAG,WAAW,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;QAC5C,MAAM,WAAW,GAAG,QAAQ,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;QACrC,MAAM,QAAQ,GAAG,WAAW,CAAC,UAAU,CAAC,KAAK,EAAE,EAAE,CAAC,CAAA;QAClD,OAAO,EAAE,EAAE,EAAE,WAAW,EAAE,cAAc,EAAE,QAAQ,EAAE,CAAA;IACtD,CAAC,CAAC,CAAA;AACN,CAAC;AACD,MAAM,CAAC,OAAO,OAAO,QAAQ;IACnB,GAAG,CAAqC;IAChD,YAAY,IAAY;QACtB,IAAI,CAAC,GAAG,GAAG;YACT,OAAO,EAAE,MAAM,CAAC,WAAW,CACzB,eAAe,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,QAAQ,CAAC,CAAC,CACnD;SACF,CAAA;IACH,CAAC;IAED,MAAM;QACJ,OAAO,IAAI,CAAC,GAAG,CAAA;IACjB,CAAC;IAED,UAAU;QACR,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,QAAQ;QACN,OAAO,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;IACtC,CAAC;IAED,MAAM,CAAC,IAAY;QACjB,OAAO,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,IAAI,CAAC,IAAI,EAAE,CAAA;IACrC,CAAC;IAED,QAAQ;QACN,MAAM,IAAI,GAAG,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,CAAE,CAAA;QAC9C,OAAO,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,MAAM,CAAA;IACjC,CAAC;IAED,aAAa;QACX,OAAO,EAAE,CAAA;IACX,CAAC;IAED,IAAI,cAAc;QAChB,OAAO,EAAE,CAAA;IACX,CAAC;IAED,SAAS;QACP,OAAO,EAAE,CAAA;IACX,CAAC;IAED,OAAO;QACL,OAAO;YACL,EAAE,EAAE,MAAM;YACV,IAAI,EAAE,MAAM;YACZ,MAAM,EAAE,IAAI;YACZ,QAAQ,EAAE,IAAI,CAAC,QAAQ,EAAE,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;gBACrC,EAAE,EAAE,IAAI;gBACR,QAAQ,EAAE,EAAE;gBACZ,IAAI;aACL,CAAC,CAAC;SACJ,CAAA;IACH,CAAC;IAED,IAAI,YAAY;QACd,OAAO,SAAS,CAAA;IAClB,CAAC;IACD,IAAI,2BAA2B;QAC7B,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,IAAI,MAAM;QACR,OAAO,EAAE,CAAA;IACX,CAAC;CACF"}

package/dist/parsers/StockholmMSA.js

@@ -71,9 +71,9 @@ 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/dist/parsers/StockholmMSA.js.map

@@ -1 +1 @@
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+{"version":3,"file":"StockholmMSA.js","sourceRoot":"","sources":["../../src/parsers/StockholmMSA.ts"],"names":[],"mappings":"AAAA,OAAO,SAAS,MAAM,cAAc,CAAA;AACpC,OAAO,WAAW,MAAM,gBAAgB,CAAA;AAExC,OAAO,EAAoB,eAAe,EAAE,MAAM,SAAS,CAAA;AAiB3D,MAAM,CAAC,OAAO,OAAO,YAAY;IACvB,IAAI,CAAkB;IACtB,GAAG,CAAgB;IAE3B,YAAY,IAAY,EAAE,gBAAwB;QAChD,MAAM,GAAG,GAAG,SAAS,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;QACpC,IAAI,CAAC,IAAI,GAAG,GAAG,CAAA;QACf,IAAI,CAAC,GAAG,GAAG,GAAG,CAAC,gBAAgB,CAAC,CAAA;IAClC,CAAC;IAED,MAAM;QACJ,OAAO,IAAI,CAAC,GAAG,CAAA;IACjB,CAAC;IAED,MAAM,CAAC,IAAY;QACjB,OAAO,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,IAAI,CAAC,IAAI,EAAE,CAAA;IACrC,CAAC;IAED,QAAQ;QACN,MAAM,IAAI,GAAG,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,CAAE,CAAA;QAC9C,OAAO,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,MAAM,CAAA;IACjC,CAAC;IAED,IAAI,cAAc;QAChB,OAAO,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,GAAG,EAAE,GAAG,EAAE,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,aAAa,GAAG,GAAG,CAAC,EAAE,CAAC,CAAA;IAC9E,CAAC;IAED,SAAS;QACP,OAAO;YACL,OAAO,EAAE,IAAI,CAAC,GAAG,CAAC,EAAE;YACpB,UAAU,EAAE,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,EAAE;YAC3B,MAAM,EAAE,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,EAAE;SACxB,CAAA;IACH,CAAC;IAED,UAAU,CAAC,OAAe;QACxB,OAAO;YACL,IAAI,EAAE,OAAO;YACb,SAAS,EAAE,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,EAAE,CAAC,OAAO,CAAC;YACnC,MAAM,EAAE,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,EAAE,EAAE,CAAC,OAAO,CAAC;SACnC,CAAA;IACH,CAAC;IAED,QAAQ;QACN,OAAO,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;IACtC,CAAC;IAED,YAAY,KAAI,CAAC;IAEjB,aAAa;QACX,MAAM,QAAQ,GAAG,sCAAsC,CAAA;QACvD,MAAM,GAAG,GAAG,IAAI,CAAC,GAAG,CAAA;QACpB,MAAM,IAAI,GAAG,MAAM,CAAC,OAAO,CAAC,GAAG,CAAC,EAAE,EAAE,EAAE,IAAI,EAAE,CAAC;aAC1C,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,EAAE,EAAE,QAAQ,CAAC,IAAI,CAAC,EAAE,CAAC,CAAU,CAAC;aACnD,MAAM,CAAC,CAAC,IAAI,EAAqC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;aAC9D,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,KAAK,CAAC,EAAE,EAAE;YACnB,MAAM,GAAG,GAAG,KAAK,CAAC,CAAC,CAAE,CAAC,WAAW,EAAE,CAAA;YACnC,MAAM,KAAK,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;YACvB,MAAM,QAAQ,GAAG,CAAC,KAAK,CAAC,CAAC,CAAE,CAAA;YAC3B,MAAM,MAAM,GAAG,CAAC,KAAK,CAAC,CAAC,CAAE,CAAA;YACzB,OAAO,EAAE,EAAE,EAAE,GAAG,EAAE,KAAK,EAAE,QAAQ,EAAE,MAAM,EAAE,CAAA;QAC7C,CAAC,CAAC,CAAA;QAEJ,MAAM,GAAG,GAAG,EAAoD,CAAA;QAChE,KAAK,MAAM,KAAK,IAAI,IAAI,EAAE,CAAC;YACzB,MAAM,EAAE,EAAE,EAAE,GAAG,IAAI,EAAE,GAAG,KAAK,CAAA;YAC7B,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,CAAC;gBACb,GAAG,CAAC,EAAE,CAAC,GAAG,EAAE,CAAA;YACd,CAAC;YACD,GAAG,CAAC,EAAE,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QACpB,CAAC;QACD,OAAO,GAAG,CAAA;IACZ,CAAC;IAED,OAAO;QACL,MAAM,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAA;QAChC,OAAO,IAAI;YACT,CAAC,CAAC,eAAe,CAAC,WAAW,CAAC,IAAI,CAAC,CAAC;YACpC,CAAC,CAAC;gBACE,EAAE,EAAE,MAAM;gBACV,IAAI,EAAE,MAAM;gBACZ,MAAM,EAAE,IAAI;gBACZ,QAAQ,EAAE,IAAI,CAAC,QAAQ,EAAE,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;oBACrC,EAAE,EAAE,IAAI;oBACR,QAAQ,EAAE,EAAE;oBACZ,IAAI;iBACL,CAAC,CAAC;aACJ,CAAA;IACP,CAAC;IAED,IAAI,YAAY;QACd,OAAO,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,QAAQ,CAAA;IAC9B,CAAC;IACD,IAAI,2BAA2B;QAC7B,OAAO,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,OAAO,CAAA;IAC7B,CAAC;IAED,IAAI,MAAM;QACR,OAAO;YACL;gBACE,EAAE,EAAE,cAAc;gBAClB,IAAI,EAAE,oBAAoB;gBAC1B,IAAI,EAAE,IAAI,CAAC,YAAY;gBACvB,iBAAiB,EAAE,EAAE;aACtB;YACD;gBACE,EAAE,EAAE,iBAAiB;gBACrB,IAAI,EAAE,qBAAqB;gBAC3B,IAAI,EAAE,IAAI,CAAC,2BAA2B;gBACtC,iBAAiB,EAAE;oBACjB,GAAG,EAAE,MAAM;oBACX,GAAG,EAAE,WAAW;iBACjB;aACF;SACF,CAAA;IACH,CAAC;CACF"}

package/dist/reparseTree.js

@@ -1,10 +1,10 @@
 export function reparseTree(tree) {
     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/dist/reparseTree.js.map

@@ -1 +1 @@
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+{"version":3,"file":"reparseTree.js","sourceRoot":"","sources":["../src/reparseTree.ts"],"names":[],"mappings":"AAEA,MAAM,UAAU,WAAW,CAAC,IAAiB;IAC3C,OAAO;QACL,GAAG,IAAI;QACP,QAAQ,EAAE,IAAI,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAC9B,CAAC,CAAC,QAAQ,CAAC,MAAM;YACf,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC;YAChB,CAAC,CAAC;gBACE,QAAQ,EAAE,CAAC,CAAC,CAAC;gBACb,EAAE,EAAE,GAAG,CAAC,CAAC,EAAE,WAAW;gBACtB,IAAI,EAAE,GAAG,CAAC,CAAC,IAAI,SAAS;aACzB,CACN;KACF,CAAA;AACH,CAAC"}

package/dist/util.d.ts

@@ -4,21 +4,21 @@ export declare function transform<T>(obj: Record<string, T>, cb: (arg0: [string,
     [k: string]: 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;
 }

package/dist/util.js

@@ -11,7 +11,7 @@ export function generateNodeIds(tree, parent = 'node', depth = 0) {
         ...tree,
         id,
         name: tree.name || id,
-        branchset: tree.branchset?.map((b, i) => generateNodeIds(b, `${id}-${i}`, depth + 1)) || [],
+        children: tree.children?.map((b, i) => generateNodeIds(b, `${id}-${i}`, depth + 1)) || [],
     };
 }
 export function colorContrast(colorScheme, theme) {

package/dist/util.js.map

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package/dist/version.d.ts

@@ -1 +1 @@
-export declare const version = "3.2.1";
+export declare const version = "3.2.2";

package/dist/version.js

@@ -1,2 +1,2 @@
-export const version = '3.2.1';
+export const version = '3.2.2';
 //# sourceMappingURL=version.js.map

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "react-msaview",
   "author": "Colin",
-  "version": "3.2.1",
+  "version": "3.2.2",
   "license": "MIT",
   "main": "dist/index.js",
   "module": "dist/index.js",
@@ -38,14 +38,15 @@
   },
   "dependencies": {
     "@eslint/js": "^9.8.0",
-    "@mui/icons-material": "^5.16.6",
-    "@mui/material": "^5.16.6",
+    "@mui/icons-material": "^5.0.0",
+    "@mui/material": "^5.0.0",
     "@types/node": "^22.1.0",
     "clustal-js": "^2.0.0",
     "colord": "^2.9.3",
     "copy-to-clipboard": "^3.3.1",
     "d3-array": "^3.2.3",
     "d3-hierarchy": "^3.1.2",
+    "emf-js": "^2.0.0",
     "eslint": "^9.8.0",
     "file-saver": "^2.0.5",
     "pako": "^2.1.0",

package/src/components/msa/renderMSABlock.ts

@@ -110,35 +110,37 @@ function drawTiles({
       data: { name },
     } = node
     const y = node.x!
-    const str = columns[name]!.slice(xStart, xEnd)
-    for (let i = 0; i < str.length; i++) {
-      const letter = str[i]!
-      const color =
-        colorSchemeName === 'clustalx_protein_dynamic'
-          ? getClustalXColor(
-              colStats[xStart + i]!,
-              colStatsSums[xStart + i]!,
-              model,
-              name,
-              xStart + i,
-            )
-          : colorSchemeName === 'percent_identity_dynamic'
-            ? getPercentIdentityColor(
+    const str = columns[name]?.slice(xStart, xEnd)
+    if (str) {
+      for (let i = 0; i < str.length; i++) {
+        const letter = str[i]!
+        const color =
+          colorSchemeName === 'clustalx_protein_dynamic'
+            ? getClustalXColor(
                 colStats[xStart + i]!,
                 colStatsSums[xStart + i]!,
                 model,
                 name,
                 xStart + i,
               )
-            : colorScheme[letter.toUpperCase()]
-      if (bgColor) {
-        ctx.fillStyle = color || theme.palette.background.default
-        ctx.fillRect(
-          i * colWidth + offsetX - (offsetX % colWidth),
-          y - rowHeight,
-          colWidth,
-          rowHeight,
-        )
+            : colorSchemeName === 'percent_identity_dynamic'
+              ? getPercentIdentityColor(
+                  colStats[xStart + i]!,
+                  colStatsSums[xStart + i]!,
+                  model,
+                  name,
+                  xStart + i,
+                )
+              : colorScheme[letter.toUpperCase()]
+        if (bgColor) {
+          ctx.fillStyle = color || theme.palette.background.default
+          ctx.fillRect(
+            i * colWidth + offsetX - (offsetX % colWidth),
+            y - rowHeight,
+            colWidth,
+            rowHeight,
+          )
+        }
       }
     }
   }
@@ -178,22 +180,24 @@ function drawText({
         data: { name },
       } = node
       const y = node.x!
-      const str = columns[name]!.slice(xStart, xEnd)
-      for (let i = 0; i < str.length; i++) {
-        const letter = str[i]!
-        const color = colorScheme[letter.toUpperCase()]
-        const contrast = contrastLettering
-          ? contrastScheme[letter.toUpperCase()] || 'black'
-          : 'black'
-        const x = i * colWidth + offsetX - (offsetX % colWidth)
+      const str = columns[name]?.slice(xStart, xEnd)
+      if (str) {
+        for (let i = 0; i < str.length; i++) {
+          const letter = str[i]!
+          const color = colorScheme[letter.toUpperCase()]
+          const contrast = contrastLettering
+            ? contrastScheme[letter.toUpperCase()] || 'black'
+            : 'black'
+          const x = i * colWidth + offsetX - (offsetX % colWidth)
 
-        // note: -rowHeight/4 matches +rowHeight/4 in tree
-        ctx.fillStyle = actuallyShowDomains
-          ? 'black'
-          : bgColor
-            ? contrast
-            : color || 'black'
-        ctx.fillText(letter, x + colWidth / 2, y - rowHeight / 4)
+          // note: -rowHeight/4 matches +rowHeight/4 in tree
+          ctx.fillStyle = actuallyShowDomains
+            ? 'black'
+            : bgColor
+              ? contrast
+              : color || 'black'
+          ctx.fillText(letter, x + colWidth / 2, y - rowHeight / 4)
+        }
       }
     }
   }

package/src/components/tree/dialogs/TreeNodeInfoDialog.tsx

@@ -24,7 +24,7 @@ const TreeNodeInfoDialog = observer(function ({
 }) {
   const { treeMetadata, rows } = model
   const metadata = treeMetadata[nodeName]
-  const [name, sequence] = rows.find(f => f[0] === nodeName)!
+  const res = rows.find(f => f[0] === nodeName)
   return (
     <Dialog
       onClose={() => {
@@ -39,7 +39,11 @@ const TreeNodeInfoDialog = observer(function ({
           <Attributes attributes={{ nodeName, ...info }} />
         </BaseCard>
         <BaseCard title="Sequence">
-          <SequenceTextArea str={[[name, sequence]]} />
+          {res ? (
+            <SequenceTextArea str={[res]} />
+          ) : (
+            <div>Sequence not found</div>
+          )}
         </BaseCard>
         {metadata ? (
           <BaseCard title="Extra metadata">

package/src/components/tree/renderTreeCanvas.ts

@@ -147,8 +147,6 @@ export function renderTreeLabels({
     marginLeft,
     leaves,
     noTree,
-    // eslint-disable-next-line  @typescript-eslint/no-unused-vars
-    rowHeight: _rowHeight, // this is needed for redrawing after zoom change
   } = model
   const by = blockSizeYOverride || blockSize
   if (labelsAlignRight) {
@@ -250,6 +248,8 @@ export function renderTreeCanvas({
     showTreeText,
     marginLeft,
     nref,
+    // eslint-disable-next-line  @typescript-eslint/no-unused-vars
+    rowHeight: _rowHeight, // this is needed for redrawing after zoom change
   } = model
   const by = blockSizeYOverride || blockSize
 

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