react-msaview 3.2.0 → 3.2.2

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,CAAC,CAAC,GAAG,CAAC,MAAM,CAAA;IACpC,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

@@ -15,7 +15,7 @@ export default class FastaMSA {
     MSA;
     constructor(text) {
         this.MSA = {
-            seqdata: Object.fromEntries(parseSmallFasta(text).map(m => [`${m.id}`, m.sequence])),
+            seqdata: Object.fromEntries(parseSmallFasta(text).map(m => [m.id, m.sequence])),
         };
     }
     getMSA() {
@@ -28,10 +28,10 @@ export default class FastaMSA {
         return Object.keys(this.MSA.seqdata);
     }
     getRow(name) {
-        return this.MSA?.seqdata[name] || '';
+        return this.MSA.seqdata[name] || '';
     }
     getWidth() {
-        const name = Object.keys(this.MSA?.seqdata)[0];
+        const name = Object.keys(this.MSA.seqdata)[0];
         return this.getRow(name).length;
     }
     getStructures() {
@@ -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,OAAO,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;QAC/C,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,GAAG,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC,QAAQ,CAAC,CAAC,CACxD;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,EAAE,OAAO,CAAC,IAAI,CAAC,IAAI,EAAE,CAAA;IACtC,CAAC;IAED,QAAQ;QACN,MAAM,IAAI,GAAG,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,EAAE,OAAO,CAAC,CAAC,CAAC,CAAC,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.d.ts

@@ -4,9 +4,9 @@ interface StockholmEntry {
         DE?: string[];
         NH?: string[];
     };
-    gs: {
+    gs?: {
         AC: Record<string, string>;
-        DR: Record<string, string>;
+        DR?: Record<string, string>;
     };
     gc?: {
         SS_cons?: string;
@@ -27,13 +27,13 @@ export default class StockholmMSA {
             DE?: string[];
             NH?: string[];
         };
-        Accessions: Record<string, string>;
-        Dbxref: Record<string, string>;
+        Accessions: Record<string, string> | undefined;
+        Dbxref: Record<string, string> | undefined;
     };
     getRowData(rowName: string): {
         name: string;
-        accession: string;
-        dbxref: string;
+        accession: string | undefined;
+        dbxref: string | undefined;
     };
     getNames(): string[];
     getSeqCoords(): void;

package/dist/parsers/StockholmMSA.js

@@ -13,10 +13,10 @@ export default class StockholmMSA {
         return this.MSA;
     }
     getRow(name) {
-        return this.MSA?.seqdata[name] || '';
+        return this.MSA.seqdata[name] || '';
     }
     getWidth() {
-        const name = Object.keys(this.MSA?.seqdata)[0];
+        const name = Object.keys(this.MSA.seqdata)[0];
         return this.getRow(name).length;
     }
     get alignmentNames() {
@@ -32,7 +32,7 @@ export default class StockholmMSA {
     getRowData(rowName) {
         return {
             name: rowName,
-            accession: this.MSA.gs?.AC?.[rowName],
+            accession: this.MSA.gs?.AC[rowName],
             dbxref: this.MSA.gs?.DR?.[rowName],
         };
     }
@@ -64,16 +64,16 @@ export default class StockholmMSA {
         return ret;
     }
     getTree() {
-        const tree = this.MSA?.gf?.NH?.[0];
+        const tree = this.MSA.gf.NH?.[0];
         return tree
             ? generateNodeIds(parseNewick(tree))
             : {
                 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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package/dist/renderToSvg.js

@@ -1,3 +1,4 @@
+/* eslint-disable react-refresh/only-export-components */
 import React from 'react';
 import { createRoot } from 'react-dom/client';
 import { when } from 'mobx';
@@ -84,12 +85,8 @@ function CoreRendering({ model, theme, width, height, offsetX, offsetY, Context,
         React.createElement("defs", null,
             React.createElement("clipPath", { id: clipId2 },
                 React.createElement("rect", { x: 0, y: 0, width: msaAreaWidth, height: height }))),
-        React.createElement("g", { clipPath: `url(#${clipId1})`, 
-            /* eslint-disable-next-line react/no-danger */
-            dangerouslySetInnerHTML: { __html: ctx1.getSvg().innerHTML } }),
-        React.createElement("g", { clipPath: `url(#${clipId2})`, transform: `translate(${treeAreaWidth} 0)`, 
-            /* eslint-disable-next-line react/no-danger */
-            dangerouslySetInnerHTML: { __html: ctx2.getSvg().innerHTML } })));
+        React.createElement("g", { clipPath: `url(#${clipId1})`, dangerouslySetInnerHTML: { __html: ctx1.getSvg().innerHTML } }),
+        React.createElement("g", { clipPath: `url(#${clipId2})`, transform: `translate(${treeAreaWidth} 0)`, dangerouslySetInnerHTML: { __html: ctx2.getSvg().innerHTML } })));
 }
 function MinimapWrapper({ model, children, }) {
     const { minimapHeight, treeAreaWidth } = model;

package/dist/renderToSvg.js.map

@@ -1 +1 @@
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+{"version":3,"file":"renderToSvg.js","sourceRoot":"","sources":["../src/renderToSvg.tsx"],"names":[],"mappings":"AAAA,yDAAyD;AACzD,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,UAAU,EAAE,MAAM,kBAAkB,CAAA;AAC7C,OAAO,EAAE,IAAI,EAAE,MAAM,MAAM,CAAA;AAC3B,OAAO,EAAE,oBAAoB,EAAE,MAAM,oBAAoB,CAAA;AAKzD,OAAO,EAAE,gBAAgB,EAAE,MAAM,oCAAoC,CAAA;AACrE,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAA;AAChE,OAAO,EAAE,aAAa,EAAE,MAAM,QAAQ,CAAA;AAEtC,OAAO,UAAU,MAAM,iCAAiC,CAAA;AACxD,OAAO,EAAE,2BAA2B,EAAE,MAAM,8CAA8C,CAAA;AAE1F,MAAM,CAAC,KAAK,UAAU,WAAW,CAC/B,KAAmB,EACnB,IAAoE;IAEpE,MAAM,IAAI,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC,KAAK,CAAC,eAAe,CAAC,CAAA;IACzC,MAAM,EAAE,KAAK,EAAE,MAAM,EAAE,OAAO,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;IACjD,MAAM,EAAE,UAAU,EAAE,KAAK,EAAE,cAAc,EAAE,GAAG,IAAI,CAAA;IAElD,IAAI,UAAU,KAAK,QAAQ,EAAE,CAAC;QAC5B,OAAO,MAAM,CAAC;YACZ,KAAK,EAAE,KAAK,CAAC,UAAU,GAAG,KAAK,CAAC,aAAa;YAC7C,MAAM,EAAE,KAAK,CAAC,WAAW;YACzB,KAAK;YACL,KAAK;YACL,OAAO,EAAE,CAAC;YACV,OAAO,EAAE,CAAC;YACV,cAAc;SACf,CAAC,CAAA;IACJ,CAAC;IACD,IAAI,UAAU,KAAK,UAAU,EAAE,CAAC;QAC9B,OAAO,MAAM,CAAC;YACZ,KAAK;YACL,MAAM;YACN,KAAK;YACL,KAAK;YACL,OAAO,EAAE,OAAO;YAChB,OAAO,EAAE,CAAC,OAAO;YACjB,cAAc;SACf,CAAC,CAAA;IACJ,CAAC;IACD,MAAM,IAAI,KAAK,CAAC,qBAAqB,CAAC,CAAA;AACxC,CAAC;AAED,KAAK,UAAU,MAAM,CAAC,EACpB,KAAK,EACL,MAAM,EACN,OAAO,EACP,OAAO,EACP,KAAK,EACL,KAAK,EACL,cAAc,GASf;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,MAAM,MAAM,CAAC,WAAW,CAAC,CAAA;IAC7C,MAAM,OAAO,GAAG,cAAc,CAAC,CAAC,CAAC,cAAc,CAAC,CAAC,CAAC,WAAW,CAAA;IAE7D,OAAO,oBAAoB,CACzB,oBAAC,UAAU,IAAC,KAAK,EAAE,KAAK,EAAE,MAAM,EAAE,MAAM;QACtC,oBAAC,OAAO,IAAC,KAAK,EAAE,KAAK;YACnB,oBAAC,aAAa,IACZ,OAAO,EAAE,OAAO,EAChB,KAAK,EAAE,KAAK,EACZ,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,OAAO,EAChB,OAAO,EAAE,OAAO,EAChB,KAAK,EAAE,KAAK,EACZ,MAAM,EAAE,MAAM,GACd,CACM,CACC,EACb,UAAU,CACX,CAAA;AACH,CAAC;AAED,SAAS,aAAa,CAAC,EACrB,KAAK,EACL,KAAK,EACL,KAAK,EACL,MAAM,EACN,OAAO,EACP,OAAO,EACP,OAAO,GAYR;IACC,MAAM,OAAO,GAAG,MAAM,CAAA;IACtB,MAAM,OAAO,GAAG,KAAK,CAAA;IACrB,MAAM,EAAE,aAAa,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IAC5C,MAAM,cAAc,GAAG,aAAa,CAAC,WAAW,EAAE,KAAK,CAAC,CAAA;IACxD,MAAM,IAAI,GAAG,OAAO,CAAC,KAAK,EAAE,MAAM,CAAC,CAAA;IACnC,MAAM,IAAI,GAAG,OAAO,CAAC,KAAK,EAAE,MAAM,CAAC,CAAA;IACnC,2BAA2B,CAAC;QAC1B,GAAG,EAAE,IAAI;QACT,OAAO;QACP,OAAO;QACP,KAAK;QACL,kBAAkB,EAAE,MAAM;QAC1B,0BAA0B,EAAE,CAAC;KAC9B,CAAC,CAAA;IACF,MAAM,YAAY,GAAG,KAAK,GAAG,aAAa,CAAA;IAC1C,gBAAgB,CAAC;QACf,KAAK;QACL,OAAO;QACP,GAAG,EAAE,IAAI;QACT,KAAK;QACL,kBAAkB,EAAE,MAAM;QAC1B,0BAA0B,EAAE,CAAC;KAC9B,CAAC,CAAA;IACF,cAAc,CAAC;QACb,KAAK;QACL,KAAK;QACL,OAAO;QACP,OAAO;QACP,cAAc;QACd,GAAG,EAAE,IAAI;QACT,kBAAkB,EAAE,YAAY;QAChC,kBAAkB,EAAE,MAAM;QAC1B,0BAA0B,EAAE,CAAC;KAC9B,CAAC,CAAA;IACF,OAAO,CACL;QACE;YACE,kCAAU,EAAE,EAAE,OAAO;gBACnB,8BAAM,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,KAAK,EAAE,aAAa,EAAE,MAAM,EAAE,MAAM,GAAI,CACjD,CACN;QACP;YACE,kCAAU,EAAE,EAAE,OAAO;gBACnB,8BAAM,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,KAAK,EAAE,YAAY,EAAE,MAAM,EAAE,MAAM,GAAI,CAChD,CACN;QAEP,2BACE,QAAQ,EAAE,QAAQ,OAAO,GAAG,EAC5B,uBAAuB,EAAE,EAAE,MAAM,EAAE,IAAI,CAAC,MAAM,EAAE,CAAC,SAAS,EAAE,GAC5D;QACF,2BACE,QAAQ,EAAE,QAAQ,OAAO,GAAG,EAC5B,SAAS,EAAE,aAAa,aAAa,KAAK,EAC1C,uBAAuB,EAAE,EAAE,MAAM,EAAE,IAAI,CAAC,MAAM,EAAE,CAAC,SAAS,EAAE,GAC5D,CACD,CACJ,CAAA;AACH,CAAC;AAED,SAAS,cAAc,CAAC,EACtB,KAAK,EACL,QAAQ,GAIT;IACC,MAAM,EAAE,aAAa,EAAE,aAAa,EAAE,GAAG,KAAK,CAAA;IAE9C,OAAO,CACL;QACE,2BAAG,SAAS,EAAE,aAAa,aAAa,KAAK;YAC3C,oBAAC,UAAU,IAAC,KAAK,EAAE,KAAK,GAAI,CAC1B;QAEJ,2BAAG,SAAS,EAAE,eAAe,aAAa,GAAG,IAAG,QAAQ,CAAK,CAC5D,CACJ,CAAA;AACH,CAAC;AAED,SAAS,UAAU,CAAC,EAClB,KAAK,EACL,MAAM,EACN,QAAQ,GAKT;IACC,OAAO,CACL,6BACE,KAAK,EAAE,KAAK,EACZ,MAAM,EAAE,MAAM,EACd,KAAK,EAAC,4BAA4B,EAClC,UAAU,EAAC,8BAA8B,EACzC,OAAO,EAAE,CAAC,CAAC,EAAE,CAAC,EAAE,KAAK,EAAE,MAAM,CAAC,CAAC,QAAQ,EAAE,IAExC,QAAQ,CACL,CACP,CAAA;AACH,CAAC;AAED,SAAS,WAAW,CAAC,EAAE,QAAQ,EAAiC;IAC9D,OAAO,QAAQ,CAAA;AACjB,CAAC"}

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

@@ -0,0 +1,2 @@
+export declare function mouseOverCoordToGlobalCoord(blanks: number[], pos: number): number;
+export declare function globalCoordToRowSpecificCoord(seq: string, pos: number): number;

package/dist/rowCoordinateCalculations.js

@@ -0,0 +1,26 @@
+export function mouseOverCoordToGlobalCoord(blanks, pos) {
+    let i = 0; // 'mouse over coord'
+    let j = 0; // 'position in blanks array'
+    let k = 0; // 'global coord'/return value
+    for (; i < pos; i++, k++) {
+        // skip multiple gaps in a row
+        while (j < blanks.length && blanks[j] - 1 === k) {
+            j++;
+            k++;
+        }
+    }
+    return k;
+}
+export function globalCoordToRowSpecificCoord(seq, pos) {
+    let k = 0;
+    for (let i = 0; i < pos; i++) {
+        if (seq[i] !== '-') {
+            k++;
+        }
+        else if (k >= pos) {
+            break;
+        }
+    }
+    return k;
+}
+//# sourceMappingURL=rowCoordinateCalculations.js.map

package/dist/rowCoordinateCalculations.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"rowCoordinateCalculations.js","sourceRoot":"","sources":["../src/rowCoordinateCalculations.ts"],"names":[],"mappings":"AAAA,MAAM,UAAU,2BAA2B,CAAC,MAAgB,EAAE,GAAW;IACvE,IAAI,CAAC,GAAG,CAAC,CAAA,CAAC,qBAAqB;IAC/B,IAAI,CAAC,GAAG,CAAC,CAAA,CAAC,6BAA6B;IACvC,IAAI,CAAC,GAAG,CAAC,CAAA,CAAC,8BAA8B;IAExC,OAAO,CAAC,GAAG,GAAG,EAAE,CAAC,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC;QACzB,8BAA8B;QAC9B,OAAO,CAAC,GAAG,MAAM,CAAC,MAAM,IAAI,MAAM,CAAC,CAAC,CAAE,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC;YACjD,CAAC,EAAE,CAAA;YACH,CAAC,EAAE,CAAA;QACL,CAAC;IACH,CAAC;IACD,OAAO,CAAC,CAAA;AACV,CAAC;AAED,MAAM,UAAU,6BAA6B,CAAC,GAAW,EAAE,GAAW;IACpE,IAAI,CAAC,GAAG,CAAC,CAAA;IACT,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,GAAG,EAAE,CAAC,EAAE,EAAE,CAAC;QAC7B,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,GAAG,EAAE,CAAC;YACnB,CAAC,EAAE,CAAA;QACL,CAAC;aAAM,IAAI,CAAC,IAAI,GAAG,EAAE,CAAC;YACpB,MAAK;QACP,CAAC;IACH,CAAC;IACD,OAAO,CAAC,CAAA;AACV,CAAC"}

package/dist/rowCoordinateCalculations.test.d.ts

@@ -0,0 +1 @@
+export {};

package/dist/rowCoordinateCalculations.test.js

@@ -0,0 +1,18 @@
+import { expect, test } from 'vitest';
+import { mouseOverCoordToGlobalCoord } from './rowCoordinateCalculations';
+test('blanks3', () => {
+    const blanks = [2, 5, 8];
+    [
+        [0, 0],
+        [1, 1],
+        [2, 3],
+        [3, 4],
+        [4, 6],
+        [5, 7],
+        [6, 9],
+        [7, 10],
+    ].forEach(r => {
+        expect(mouseOverCoordToGlobalCoord(blanks, r[0])).toBe(r[1]);
+    });
+});
+//# sourceMappingURL=rowCoordinateCalculations.test.js.map

package/dist/rowCoordinateCalculations.test.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"rowCoordinateCalculations.test.js","sourceRoot":"","sources":["../src/rowCoordinateCalculations.test.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,QAAQ,CAAA;AACrC,OAAO,EAAE,2BAA2B,EAAE,MAAM,6BAA6B,CAAA;AACzE,IAAI,CAAC,SAAS,EAAE,GAAG,EAAE;IACnB,MAAM,MAAM,GAAG,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC,CACvB;IACC;QACE,CAAC,CAAC,EAAE,CAAC,CAAC;QACN,CAAC,CAAC,EAAE,CAAC,CAAC;QACN,CAAC,CAAC,EAAE,CAAC,CAAC;QACN,CAAC,CAAC,EAAE,CAAC,CAAC;QACN,CAAC,CAAC,EAAE,CAAC,CAAC;QACN,CAAC,CAAC,EAAE,CAAC,CAAC;QACN,CAAC,CAAC,EAAE,CAAC,CAAC;QACN,CAAC,CAAC,EAAE,EAAE,CAAC;KAEV,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE;QACZ,MAAM,CAAC,2BAA2B,CAAC,MAAM,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAC9D,CAAC,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA"}

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

@@ -1 +1 @@
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+{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,GAAG,EAAE,MAAM,UAAU,CAAA;AAE9B,OAAO,EAAE,MAAM,EAAE,MAAM,EAAE,MAAM,QAAQ,CAAA;AACvC,OAAO,WAAW,MAAM,sBAAsB,CAAA;AAE9C,MAAM,CAAC,CAAC,WAAW,CAAC,CAAC,CAAA;AAErB,MAAM,UAAU,SAAS,CACvB,GAAsB,EACtB,EAAsC;IAEtC,OAAO,MAAM,CAAC,WAAW,CAAC,MAAM,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,CAAA;AACxD,CAAC;AAwBD,MAAM,UAAU,eAAe,CAC7B,IAAU,EACV,MAAM,GAAG,MAAM,EACf,KAAK,GAAG,CAAC;IAET,MAAM,EAAE,GAAG,GAAG,MAAM,IAAI,KAAK,EAAE,CAAA;IAE/B,OAAO;QACL,GAAG,IAAI;QACP,EAAE;QACF,IAAI,EAAE,IAAI,CAAC,IAAI,IAAI,EAAE;QACrB,QAAQ,EACN,IAAI,CAAC,QAAQ,EAAE,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAC1B,eAAe,CAAC,CAAC,EAAE,GAAG,EAAE,IAAI,CAAC,EAAE,EAAE,KAAK,GAAG,CAAC,CAAC,CAC5C,IAAI,EAAE;KACV,CAAA;AACH,CAAC;AAED,MAAM,UAAU,aAAa,CAC3B,WAAmC,EACnC,KAAY;IAEZ,OAAO,SAAS,CAAC,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,KAAK,CAAC,EAAE,EAAE,CAAC;QACjD,MAAM;QACN,KAAK,CAAC,OAAO,CAAC,eAAe,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,KAAK,EAAE,CAAC;KACrD,CAAC,CAAA;AACJ,CAAC;AAED,MAAM,UAAU,UAAU,CAAC,MAAgB,EAAE,GAAsB;IACjE,IAAI,CAAC,GAAG,EAAE,CAAA;IACV,IAAI,CAAC,GAAG,CAAC,CAAA;IACT,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QACpC,IAAI,CAAC,KAAK,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC;YACpB,CAAC,EAAE,CAAA;QACL,CAAC;aAAM,CAAC;YACN,CAAC,IAAI,GAAG,CAAC,CAAC,CAAC,CAAA;QACb,CAAC;IACH,CAAC;IACD,OAAO,CAAC,CAAA;AACV,CAAC;AAED,6EAA6E;AAC7E,MAAM,UAAU,WAAW,CACzB,CAA6B,EAC7B,EAAU,EACV,CAAS;IAET,mBAAmB;IACnB,CAAC,CAAC,GAAG,GAAG,CAAC,EAAE,IAAI,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,IAAI,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,CAAA;IAEnD,IAAI,CAAC,CAAC,QAAQ,EAAE,CAAC;QACf,CAAC,CAAC,QAAQ,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE;YACrB,WAAW,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC,CAAA;QACvB,CAAC,CAAC,CAAA;IACJ,CAAC;AACH,CAAC;AAED,6EAA6E;AAC7E,MAAM,UAAU,SAAS,CAAC,CAA6B;IACrD,OAAO,CACL,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,EAAE,SAAS,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAC1E,CAAA;AACH,CAAC;AAED,gDAAgD;AAChD,8DAA8D;AAC9D,MAAM,UAAU,QAAQ,CAAC,CAA6B;IACpD,IAAI,CAAC,CAAC,QAAQ,EAAE,CAAC;QACf,mBAAmB;QACnB,CAAC,CAAC,SAAS,GAAG,CAAC,CAAC,QAAQ,CAAA;QACxB,mBAAmB;QACnB,CAAC,CAAC,QAAQ,GAAG,IAAI,CAAA;IACnB,CAAC;AACH,CAAC;AAED,MAAM,UAAU,KAAK,CAAC,GAAW,EAAE,GAAW,EAAE,GAAW;IACzD,OAAO,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,GAAG,EAAE,GAAG,CAAC,EAAE,GAAG,CAAC,CAAA;AAC1C,CAAC;AAED,MAAM,UAAU,GAAG,CAAC,CAAiC;IACnD,OAAO,CAAC,CAAC,GAAG,GAAG,CAAC,CAAC,KAAK,CAAA;AACxB,CAAC"}

package/dist/version.d.ts

@@ -1 +1 @@
-export declare const version = "3.2.0";
+export declare const version = "3.2.2";

package/dist/version.js

@@ -1,2 +1,2 @@
-export const version = '3.2.0';
+export const version = '3.2.2';
 //# sourceMappingURL=version.js.map

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "react-msaview",
   "author": "Colin",
-  "version": "3.2.0",
+  "version": "3.2.2",
   "license": "MIT",
   "main": "dist/index.js",
   "module": "dist/index.js",
@@ -23,8 +23,7 @@
     "build": "npm run build:esm && npm run build:bundle",
     "prepack": "npm run build",
     "postversion": "git push --follow-tags",
-    "prestatedocs": "yarn tsc --build docgen/tsconfig.json",
-    "statedocs": "rm -rf apidocs && mkdir apidocs && node docgen/dist/generateStateModelDocs.js",
+    "statedocs": "rm -rf apidocs && mkdir apidocs && yarn tsx docgen/generateStateModelDocs.ts",
     "poststatedocs": "npm run format"
   },
   "peerDependencies": {
@@ -38,11 +37,17 @@
     "react-dom": ">=16.8.0"
   },
   "dependencies": {
+    "@eslint/js": "^9.8.0",
+    "@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",
     "rbush": "^3.0.1",

package/src/colorSchemes.ts

@@ -357,7 +357,7 @@ export function getClustalXColor(
   row: string,
   col: number,
 ) {
-  const l = model.columns[row][col]
+  const l = model.columns[row]![col]!
   const {
     W = 0,
     L = 0,
@@ -495,8 +495,8 @@ export function getClustalXColor(
 // info http://www.jalview.org/help/html/colourSchemes/clustal.html
 // modifications:
 // reference to clustalX source code scheme modifies what the jalview.org
-// scheme says there the jalview.org colorscheme says WLVIMAFCHP but it
-// should be WLVIMAFCHPY, colprot.xml says e.g. %#ACFHILMVWYPp" which has Y
+// scheme says there the jalview.org colorscheme says WLVIMAFCHP but it should
+// be WLVIMAFCHPY, colprot.xml says e.g. %#ACFHILMVWYPp" which has Y
 export function getPercentIdentityColor(
   stats: Record<string, number>,
   total: number,
@@ -504,7 +504,7 @@ export function getPercentIdentityColor(
   row: string,
   col: number,
 ) {
-  const l = model.columns[row][col]
+  const l = model.columns[row]![col]!
   const entries = Object.entries(stats)
   let ent = 0
   let letter = ''

package/src/components/Loading.tsx

@@ -19,7 +19,13 @@ const Reset = observer(function ({
   return (
     <div>
       <ErrorMessage error={error} />
-      <Button variant="contained" color="primary" onClick={() => model.reset()}>
+      <Button
+        variant="contained"
+        color="primary"
+        onClick={() => {
+          model.reset()
+        }}
+      >
         Return to import form
       </Button>
     </div>

package/src/components/ResizeHandles.tsx

@@ -57,7 +57,9 @@ export const VerticalResizeHandle = observer(function ({
   return (
     <div>
       <div
-        onMouseDown={() => setMouseDragging(true)}
+        onMouseDown={() => {
+          setMouseDragging(true)
+        }}
         style={{
           cursor: 'ew-resize',
           height: '100%',
@@ -123,7 +125,9 @@ export const HorizontalResizeHandle = observer(function ({
   return (
     <div>
       <div
-        onMouseDown={() => setMouseDragging(true)}
+        onMouseDown={() => {
+          setMouseDragging(true)
+        }}
         style={{
           cursor: 'ns-resize',
           width: '100%',

package/src/components/SequenceTextArea.tsx

@@ -25,7 +25,7 @@ export default function SequenceTextArea({ str }: { str: [string, string][] }) {
   const [showEmpty, setShowEmpty] = useState(false)
 
   const disp = str
-    .map(([s1, s2]) => [s1, showGaps ? s2 : s2.replaceAll('-', '')])
+    .map(([s1, s2]) => [s1, showGaps ? s2 : s2.replaceAll('-', '')] as const)
     .filter(f => (showEmpty ? true : !!f[1]))
     .map(([s1, s2]) => `>${s1}\n${showGaps ? s2 : s2.replaceAll('-', '')}`)
     .join('\n')
@@ -37,7 +37,9 @@ export default function SequenceTextArea({ str }: { str: [string, string][] }) {
         onClick={() => {
           copy(disp)
           setCopied(true)
-          setTimeout(() => setCopied(false), 500)
+          setTimeout(() => {
+            setCopied(false)
+          }, 500)
         }}
       >
         {copied ? 'Copied!' : 'Copy to clipboard'}
@@ -45,12 +47,16 @@ export default function SequenceTextArea({ str }: { str: [string, string][] }) {
       <Checkbox2
         label="Show gaps"
         checked={showGaps}
-        onChange={() => setShowGaps(!showGaps)}
+        onChange={() => {
+          setShowGaps(!showGaps)
+        }}
       />
       <Checkbox2
         label="Show empty"
         checked={showEmpty}
-        onChange={() => setShowEmpty(!showEmpty)}
+        onChange={() => {
+          setShowEmpty(!showEmpty)
+        }}
       />
       <TextField
         variant="outlined"

package/src/components/TextTrack.tsx

@@ -55,9 +55,9 @@ const AnnotationBlock = observer(function ({
 
     const xStart = Math.max(0, Math.floor(offsetX / colWidth))
     const xEnd = Math.max(0, Math.ceil((offsetX + blockSize) / colWidth))
-    const str = data?.slice(xStart, xEnd)
+    const str = data.slice(xStart, xEnd)
     for (let i = 0; str && i < str.length; i++) {
-      const letter = str[i]
+      const letter = str[i]!
       const color = colorScheme[letter.toUpperCase()]
       if (bgColor) {
         const x = i * colWidth + offsetX - (offsetX % colWidth)

package/src/components/Track.tsx

@@ -24,7 +24,7 @@ export const TrackLabel = observer(function ({
   track,
 }: {
   model: MsaViewModel
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
+
   track: any
 }) {
   const [anchorEl, setAnchorEl] = useState<HTMLButtonElement>()
@@ -53,7 +53,9 @@ export const TrackLabel = observer(function ({
           width: trackLabelHeight,
           height: trackLabelHeight,
         }}
-        onClick={event => setAnchorEl(event.currentTarget)}
+        onClick={event => {
+          setAnchorEl(event.currentTarget)
+        }}
       >
         <ArrowDropDownIcon />
       </IconButton>
@@ -62,7 +64,9 @@ export const TrackLabel = observer(function ({
           anchorEl={anchorEl}
           transitionDuration={0}
           open
-          onClose={() => setAnchorEl(undefined)}
+          onClose={() => {
+            setAnchorEl(undefined)
+          }}
         >
           <MenuItem
             dense
@@ -96,7 +100,7 @@ const Track = observer(function ({
   track,
 }: {
   model: MsaViewModel
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
+
   track: any
 }) {
   const { resizeHandleWidth } = model