react-msaview 3.1.3 → 3.1.4

package/dist/model.js.map

@@ -1 +1 @@
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package/dist/parseNewick.js

@@ -58,7 +58,6 @@
  * }
  */
 export default function parse(s) {
-    var _a;
     const ancestors = [];
     // eslint-disable-next-line @typescript-eslint/no-explicit-any
     let tree = {};
@@ -73,7 +72,7 @@ export default function parse(s) {
                 tree = subtree;
                 break;
             case ',': // another branch
-                (_a = ancestors.at(-1)) === null || _a === void 0 ? void 0 : _a.branchset.push(subtree);
+                ancestors.at(-1)?.branchset.push(subtree);
                 tree = subtree;
                 break;
             case ')': // optional name next

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;IACpB,8DAA8D;IAC9D,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,CAAC,CAAA;QACvB,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,MAAA,SAAS,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,0CAAE,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,CAAC,CAAA;gBACvB,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,UAAU,CAAC,KAAK,CAAC,CAAA;gBACjC,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;IACpB,8DAA8D;IAC9D,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,CAAC,CAAA;QACvB,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,CAAC,CAAA;gBACvB,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,UAAU,CAAC,KAAK,CAAC,CAAA;gBACjC,CAAC;YACH,CAAC;QACH,CAAC;IACH,CAAC;IACD,OAAO,IAAI,CAAA;AACb,CAAC"}

package/dist/parsers/ClustalMSA.js

@@ -1,5 +1,6 @@
 import { parse } from 'clustal-js';
 export default class ClustalMSA {
+    MSA;
     constructor(text) {
         this.MSA = parse(text);
     }
@@ -7,8 +8,7 @@ export default class ClustalMSA {
         return this.MSA;
     }
     getRow(name) {
-        var _a;
-        return ((_a = this.MSA.alns.find(aln => aln.id === name)) === null || _a === void 0 ? void 0 : _a.seq) || '';
+        return this.MSA.alns.find(aln => aln.id === name)?.seq || '';
     }
     getWidth() {
         return this.MSA.alns[0].seq.length;
@@ -47,8 +47,7 @@ export default class ClustalMSA {
         return undefined;
     }
     get tracks() {
-        var _a;
-        return ((_a = this.seqConsensus) === null || _a === void 0 ? void 0 : _a.trim())
+        return this.seqConsensus?.trim()
             ? [
                 {
                     id: 'seqConsensus',

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;IAG7B,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,CAAA,MAAA,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,KAAK,IAAI,CAAC,0CAAE,GAAG,KAAI,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,CAAA,MAAA,IAAI,CAAC,YAAY,0CAAE,IAAI,EAAE;YAC9B,CAAC,CAAC;gBACE;oBACE,EAAE,EAAE,cAAc;oBAClB,IAAI,EAAE,oBAAoB;oBAC1B,IAAI,EAAE,IAAI,CAAC,YAAY;oBACvB,iBAAiB,EAAE;wBACjB,GAAG,EAAE,OAAO;wBACZ,GAAG,EAAE,MAAM;wBACX,GAAG,EAAE,UAAU;wBACf,GAAG,EAAE,OAAO;qBACb;iBACF;aACF;YACH,CAAC,CAAC,EAAE,CAAA;IACR,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,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,IAAI,CAAC,YAAY,EAAE,IAAI,EAAE;YAC9B,CAAC,CAAC;gBACE;oBACE,EAAE,EAAE,cAAc;oBAClB,IAAI,EAAE,oBAAoB;oBAC1B,IAAI,EAAE,IAAI,CAAC,YAAY;oBACvB,iBAAiB,EAAE;wBACjB,GAAG,EAAE,OAAO;wBACZ,GAAG,EAAE,MAAM;wBACX,GAAG,EAAE,UAAU;wBACf,GAAG,EAAE,OAAO;qBACb;iBACF;aACF;YACH,CAAC,CAAC,EAAE,CAAA;IACR,CAAC;CACF"}

package/dist/parsers/FastaMSA.js

@@ -12,6 +12,7 @@ function parseSmallFasta(text) {
     });
 }
 export default class FastaMSA {
+    MSA;
     constructor(text) {
         this.MSA = {
             seqdata: Object.fromEntries(parseSmallFasta(text).map(m => [`${m.id}`, m.sequence])),
@@ -27,12 +28,10 @@ export default class FastaMSA {
         return Object.keys(this.MSA.seqdata);
     }
     getRow(name) {
-        var _a;
-        return ((_a = this.MSA) === null || _a === void 0 ? void 0 : _a.seqdata[name]) || '';
+        return this.MSA?.seqdata[name] || '';
     }
     getWidth() {
-        var _a;
-        const name = Object.keys((_a = this.MSA) === null || _a === void 0 ? void 0 : _a.seqdata)[0];
+        const name = Object.keys(this.MSA?.seqdata)[0];
         return this.getRow(name).length;
     }
     getStructures() {

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;IAE3B,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,CAAA,MAAA,IAAI,CAAC,GAAG,0CAAE,OAAO,CAAC,IAAI,CAAC,KAAI,EAAE,CAAA;IACtC,CAAC;IAED,QAAQ;;QACN,MAAM,IAAI,GAAG,MAAM,CAAC,IAAI,CAAC,MAAA,IAAI,CAAC,GAAG,0CAAE,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,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"}

package/dist/parsers/StockholmMSA.js

@@ -2,6 +2,8 @@ import Stockholm from 'stockholm-js';
 import parseNewick from '../parseNewick';
 import { generateNodeIds } from '../util';
 export default class StockholmMSA {
+    data;
+    MSA;
     constructor(text, currentAlignment) {
         const res = Stockholm.parseAll(text);
         this.data = res;
@@ -11,31 +13,27 @@ export default class StockholmMSA {
         return this.MSA;
     }
     getRow(name) {
-        var _a;
-        return ((_a = this.MSA) === null || _a === void 0 ? void 0 : _a.seqdata[name]) || '';
+        return this.MSA?.seqdata[name] || '';
     }
     getWidth() {
-        var _a;
-        const name = Object.keys((_a = this.MSA) === null || _a === void 0 ? void 0 : _a.seqdata)[0];
+        const name = Object.keys(this.MSA?.seqdata)[0];
         return this.getRow(name).length;
     }
     get alignmentNames() {
-        return this.data.map((aln, idx) => { var _a; return ((_a = aln.gf.DE) === null || _a === void 0 ? void 0 : _a[0]) || `Alignment ${idx + 1}`; });
+        return this.data.map((aln, idx) => aln.gf.DE?.[0] || `Alignment ${idx + 1}`);
     }
     getHeader() {
-        var _a, _b;
         return {
             General: this.MSA.gf,
-            Accessions: (_a = this.MSA.gs) === null || _a === void 0 ? void 0 : _a.AC,
-            Dbxref: (_b = this.MSA.gs) === null || _b === void 0 ? void 0 : _b.DR,
+            Accessions: this.MSA.gs?.AC,
+            Dbxref: this.MSA.gs?.DR,
         };
     }
     getRowData(rowName) {
-        var _a, _b, _c, _d;
         return {
             name: rowName,
-            accession: (_b = (_a = this.MSA.gs) === null || _a === void 0 ? void 0 : _a.AC) === null || _b === void 0 ? void 0 : _b[rowName],
-            dbxref: (_d = (_c = this.MSA.gs) === null || _c === void 0 ? void 0 : _c.DR) === null || _d === void 0 ? void 0 : _d[rowName],
+            accession: this.MSA.gs?.AC?.[rowName],
+            dbxref: this.MSA.gs?.DR?.[rowName],
         };
     }
     getNames() {
@@ -43,10 +41,9 @@ export default class StockholmMSA {
     }
     getSeqCoords() { }
     getStructures() {
-        var _a;
         const pdbRegex = /PDB; +(\S+) +(\S); ([0-9]+)-([0-9]+)/;
         const ent = this.MSA;
-        const args = Object.entries(((_a = ent.gs) === null || _a === void 0 ? void 0 : _a.DR) || {})
+        const args = Object.entries(ent.gs?.DR || {})
             .map(([id, dr]) => [id, pdbRegex.exec(dr)])
             .filter((item) => !!item[1])
             .map(([id, match]) => {
@@ -67,8 +64,7 @@ export default class StockholmMSA {
         return ret;
     }
     getTree() {
-        var _a, _b, _c;
-        const tree = (_c = (_b = (_a = this.MSA) === null || _a === void 0 ? void 0 : _a.gf) === null || _b === void 0 ? void 0 : _b.NH) === null || _c === void 0 ? void 0 : _c[0];
+        const tree = this.MSA?.gf?.NH?.[0];
         return tree
             ? generateNodeIds(parseNewick(tree))
             : {
@@ -83,12 +79,10 @@ export default class StockholmMSA {
             };
     }
     get seqConsensus() {
-        var _a;
-        return (_a = this.MSA.gc) === null || _a === void 0 ? void 0 : _a.seq_cons;
+        return this.MSA.gc?.seq_cons;
     }
     get secondaryStructureConsensus() {
-        var _a;
-        return (_a = this.MSA.gc) === null || _a === void 0 ? void 0 : _a.SS_cons;
+        return this.MSA.gc?.SS_cons;
     }
     get tracks() {
         return [

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,EAAe,eAAe,EAAE,MAAM,SAAS,CAAA;AAiBtD,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,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,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,EAAE,CAAC,OAAO,CAAC;YACrC,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,CAAC,CAAC,WAAW,EAAE,CAAA;YAClC,MAAM,KAAK,GAAG,KAAK,CAAC,CAAC,CAAC,CAAA;YACtB,MAAM,QAAQ,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;YAC1B,MAAM,MAAM,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;YACxB,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,EAAE,EAAE,EAAE,EAAE,EAAE,CAAC,CAAC,CAAC,CAAA;QAClC,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,SAAS,EAAE,IAAI,CAAC,QAAQ,EAAE,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;oBACtC,EAAE,EAAE,IAAI;oBACR,SAAS,EAAE,EAAE;oBACb,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/renderToSvg.js

@@ -82,6 +82,7 @@ function CoreRendering({ model, theme, width, height, offsetX, offsetY, Context,
     });
     renderMSABlock({
         model,
+        theme,
         offsetY,
         offsetX,
         contrastScheme,

package/dist/renderToSvg.js.map

@@ -1 +1 @@
-{"version":3,"file":"renderToSvg.js","sourceRoot":"","sources":["../src/renderToSvg.tsx"],"names":[],"mappings":"AAAA,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,yCAAyC,CAAA;AAC1E,OAAO,EAAE,cAAc,EAAE,MAAM,sCAAsC,CAAA;AACrE,OAAO,EAAE,aAAa,EAAE,MAAM,QAAQ,CAAA;AACtC,OAAO,UAAU,MAAM,yBAAyB,CAAA;AAEhD,MAAM,CAAC,KAAK,UAAU,WAAW,CAC/B,KAAmB,EACnB,IAAoE;IAEpE,MAAM,IAAI,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC,KAAK,CAAC,WAAW,CAAC,CAAA;IACrC,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;SAAM,IAAI,UAAU,KAAK,UAAU,EAAE,CAAC;QACrC,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;SAAM,CAAC;QACN,MAAM,IAAI,KAAK,CAAC,qBAAqB,CAAC,CAAA;IACxC,CAAC;AACH,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,iEAAiE;AACjE,4CAA4C;AAC5C,0BAA0B;AAC1B,aAAa;AACb,8BAA8B;AAC9B,eAAe;AACf,iCAAiC;AACjC,uEAAuE;AACvE,sBAAsB;AACtB,gBAAgB;AAChB,WAAW;AACX,uCAAuC;AACvC,yDAAyD;AACzD,wEAAwE;AACxE,WAAW;AACX,WAAW;AACX,sDAAsD;AACtD,yDAAyD;AACzD,wEAAwE;AACxE,WAAW;AACX,iBAAiB;AACjB,MAAM;AACN,IAAI;AAEJ,SAAS,aAAa,CAAC,EACrB,KAAK,EACL,KAAK,EACL,KAAK,EACL,MAAM,EACN,OAAO,EACP,OAAO,EACP,OAAO,GAYR;IACC,MAAM,MAAM,GAAG,MAAM,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,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,OAAO;QACP,OAAO;QACP,cAAc;QACd,GAAG,EAAE,IAAI;QACT,kBAAkB,EAAE,KAAK,GAAG,aAAa;QACzC,kBAAkB,EAAE,MAAM;QAC1B,0BAA0B,EAAE,CAAC;KAC9B,CAAC,CAAA;IACF,OAAO,CACL;QACE;YACE,kCAAU,EAAE,EAAE,MAAM;gBAClB,8BAAM,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,KAAK,EAAE,aAAa,EAAE,MAAM,EAAE,MAAM,GAAI,CACjD,CACN;QACP,2BACE,QAAQ,EAAE,QAAQ,MAAM,GAAG;YAC3B,8CAA8C;YAC9C,uBAAuB,EAAE,EAAE,MAAM,EAAE,IAAI,CAAC,MAAM,EAAE,CAAC,SAAS,EAAE,GAC5D;QACF,2BACE,SAAS,EAAE,aAAa,aAAa,KAAK;YAC1C,8CAA8C;YAC9C,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,0CAAG,QAAQ,CAAI,CAAA;AACxB,CAAC"}
+{"version":3,"file":"renderToSvg.js","sourceRoot":"","sources":["../src/renderToSvg.tsx"],"names":[],"mappings":"AAAA,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,yCAAyC,CAAA;AAC1E,OAAO,EAAE,cAAc,EAAE,MAAM,sCAAsC,CAAA;AACrE,OAAO,EAAE,aAAa,EAAE,MAAM,QAAQ,CAAA;AACtC,OAAO,UAAU,MAAM,yBAAyB,CAAA;AAEhD,MAAM,CAAC,KAAK,UAAU,WAAW,CAC/B,KAAmB,EACnB,IAAoE;IAEpE,MAAM,IAAI,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC,KAAK,CAAC,WAAW,CAAC,CAAA;IACrC,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;SAAM,IAAI,UAAU,KAAK,UAAU,EAAE,CAAC;QACrC,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;SAAM,CAAC;QACN,MAAM,IAAI,KAAK,CAAC,qBAAqB,CAAC,CAAA;IACxC,CAAC;AACH,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,iEAAiE;AACjE,4CAA4C;AAC5C,0BAA0B;AAC1B,aAAa;AACb,8BAA8B;AAC9B,eAAe;AACf,iCAAiC;AACjC,uEAAuE;AACvE,sBAAsB;AACtB,gBAAgB;AAChB,WAAW;AACX,uCAAuC;AACvC,yDAAyD;AACzD,wEAAwE;AACxE,WAAW;AACX,WAAW;AACX,sDAAsD;AACtD,yDAAyD;AACzD,wEAAwE;AACxE,WAAW;AACX,iBAAiB;AACjB,MAAM;AACN,IAAI;AAEJ,SAAS,aAAa,CAAC,EACrB,KAAK,EACL,KAAK,EACL,KAAK,EACL,MAAM,EACN,OAAO,EACP,OAAO,EACP,OAAO,GAYR;IACC,MAAM,MAAM,GAAG,MAAM,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,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,KAAK,GAAG,aAAa;QACzC,kBAAkB,EAAE,MAAM;QAC1B,0BAA0B,EAAE,CAAC;KAC9B,CAAC,CAAA;IACF,OAAO,CACL;QACE;YACE,kCAAU,EAAE,EAAE,MAAM;gBAClB,8BAAM,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,KAAK,EAAE,aAAa,EAAE,MAAM,EAAE,MAAM,GAAI,CACjD,CACN;QACP,2BACE,QAAQ,EAAE,QAAQ,MAAM,GAAG;YAC3B,8CAA8C;YAC9C,uBAAuB,EAAE,EAAE,MAAM,EAAE,IAAI,CAAC,MAAM,EAAE,CAAC,SAAS,EAAE,GAC5D;QACF,2BACE,SAAS,EAAE,aAAa,aAAa,KAAK;YAC1C,8CAA8C;YAC9C,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,0CAAG,QAAQ,CAAI,CAAA;AACxB,CAAC"}

package/dist/util.js

@@ -6,13 +6,12 @@ export function transform(obj, cb) {
     return Object.fromEntries(Object.entries(obj).map(cb));
 }
 export function generateNodeIds(tree, parent = 'node', depth = 0) {
-    var _a;
     const id = `${parent}-${depth}`;
     return {
         ...tree,
         id,
         name: tree.name || id,
-        branchset: ((_a = tree.branchset) === null || _a === void 0 ? void 0 : _a.map((b, i) => generateNodeIds(b, `${id}-${i}`, depth + 1))) || [],
+        branchset: tree.branchset?.map((b, i) => generateNodeIds(b, `${id}-${i}`, depth + 1)) || [],
     };
 }
 export function colorContrast(colorScheme, theme) {
@@ -22,7 +21,11 @@ export function colorContrast(colorScheme, theme) {
     ]);
 }
 export function parseGFF(str) {
-    return str === null || str === void 0 ? void 0 : str.split('\n').map(f => f.trim()).filter(f => !!f && !f.startsWith('#')).map(f => {
+    return str
+        ?.split('\n')
+        .map(f => f.trim())
+        .filter(f => !!f && !f.startsWith('#'))
+        .map(f => {
         const [seq_id, source, type, start, end, score, strand, phase, col9] = f.split('\t');
         return {
             seq_id,
@@ -87,7 +90,7 @@ export function collapse(d) {
 // Collapse the node and all it's children, from
 // https://bl.ocks.org/d3noob/43a860bc0024792f8803bba8ca0d5ecd
 export function filterHiddenLeafNodes(d, hiddenId) {
-    if (d === null || d === void 0 ? void 0 : d.children) {
+    if (d?.children) {
         d.children = d.children.filter(f => f.id !== hiddenId);
     }
 }

package/dist/util.js.map

@@ -1 +1 @@
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package/dist/version.d.ts

@@ -1 +1 @@
-export declare const version = "3.1.3";
+export declare const version = "3.1.4";

package/dist/version.js

@@ -1,2 +1,2 @@
-export const version = '3.1.3';
+export const version = '3.1.4';
 //# sourceMappingURL=version.js.map

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "react-msaview",
   "author": "Colin",
-  "version": "3.1.3",
+  "version": "3.1.4",
   "license": "MIT",
   "main": "dist/index.js",
   "files": [

package/src/components/ImportForm/util.ts

@@ -15,6 +15,7 @@ export async function load(
       await model.setTreeFilehandle(treeFile)
     }
   } catch (e) {
+    console.error(e)
     model.setError(e)
   }
 }

package/src/components/Loading.tsx

@@ -0,0 +1,27 @@
+import React from 'react'
+
+import { observer } from 'mobx-react'
+import { Typography } from '@mui/material'
+
+// locals
+import ImportForm from './ImportForm'
+import MSAView from './MSAView'
+import { MsaViewModel } from '../model'
+
+const Loading = observer(function ({ model }: { model: MsaViewModel }) {
+  const { done, initialized } = model
+
+  return (
+    <div>
+      {!initialized ? (
+        <ImportForm model={model} />
+      ) : !done ? (
+        <Typography variant="h4">Loading...</Typography>
+      ) : (
+        <MSAView model={model} />
+      )}
+    </div>
+  )
+})
+
+export default Loading

package/src/components/MSAPanel/MSABlock.tsx

@@ -42,13 +42,14 @@ const MSABlock = observer(function ({
     return autorun(() => {
       renderMSABlock({
         ctx,
+        theme,
         offsetX,
         offsetY,
         contrastScheme,
         model,
       })
     })
-  }, [model, offsetX, offsetY, contrastScheme])
+  }, [model, offsetX, offsetY, theme, contrastScheme])
   return (
     <canvas
       ref={ref}

package/src/components/MSAPanel/MSAMouseoverCanvas.tsx

@@ -15,17 +15,17 @@ const MSAMouseoverCanvas = observer(function ({
   const { height, width } = model
   useEffect(() => {
     const ctx = ref.current?.getContext('2d')
-    if (!ctx) {
-      return
-    }
-    return autorun(() => {
-      renderMouseover({ ctx, model })
-    })
+    return ctx
+      ? autorun(() => {
+          renderMouseover({ ctx, model })
+        })
+      : undefined
   }, [model])
 
   return (
     <canvas
       ref={ref}
+      id="mouseover"
       width={width}
       height={height}
       style={{

package/src/components/MSAPanel/index.tsx

@@ -5,9 +5,9 @@ import { MsaViewModel } from '../../model'
 
 export default function MSAPanel({ model }: { model: MsaViewModel }) {
   return (
-    <>
+    <div style={{ position: 'relative' }}>
       <MSACanvas model={model} />
       <MSAMouseoverCanvas model={model} />
-    </>
+    </div>
   )
 }

package/src/components/MSAPanel/renderMSABlock.ts

@@ -3,6 +3,7 @@ import { MsaViewModel } from '../../model'
 import { getClustalXColor, getPercentIdentityColor } from '../../colorSchemes'
 import { NodeWithIdsAndLength } from '../../util'
 import { HierarchyNode } from 'd3-hierarchy'
+import { Theme } from '@mui/material'
 
 export function renderMSABlock({
   model,
@@ -10,12 +11,14 @@ export function renderMSABlock({
   offsetY,
   contrastScheme,
   ctx,
+  theme,
   highResScaleFactorOverride,
   blockSizeXOverride,
   blockSizeYOverride,
 }: {
   offsetX: number
   offsetY: number
+  theme: Theme
   model: MsaViewModel
   contrastScheme: Record<string, string>
   ctx: CanvasRenderingContext2D
@@ -52,6 +55,7 @@ export function renderMSABlock({
   drawTiles({
     model,
     ctx,
+    theme,
     offsetX,
     offsetY,
     xStart,
@@ -63,6 +67,7 @@ export function renderMSABlock({
     ctx,
     offsetX,
     contrastScheme,
+    theme,
     xStart,
     xEnd,
     visibleLeaves,
@@ -74,11 +79,13 @@ function drawTiles({
   offsetX,
   ctx,
   visibleLeaves,
+  theme,
   xStart,
   xEnd,
 }: {
   model: MsaViewModel
   offsetX: number
+  theme: Theme
   offsetY: number
   ctx: CanvasRenderingContext2D
   visibleLeaves: HierarchyNode<NodeWithIdsAndLength>[]
@@ -118,7 +125,7 @@ function drawTiles({
             : colorScheme[letter.toUpperCase()]
       if (bgColor) {
         const x = i * colWidth + offsetX - (offsetX % colWidth)
-        ctx.fillStyle = color || 'white'
+        ctx.fillStyle = color || theme.palette.background.default
         ctx.fillRect(x, y - rowHeight, colWidth, rowHeight)
       }
     }
@@ -129,6 +136,7 @@ function drawText({
   model,
   offsetX,
   contrastScheme,
+  theme,
   ctx,
   visibleLeaves,
   xStart,
@@ -137,6 +145,7 @@ function drawText({
   offsetX: number
   model: MsaViewModel
   contrastScheme: Record<string, string>
+  theme: Theme
   ctx: CanvasRenderingContext2D
   visibleLeaves: HierarchyNode<NodeWithIdsAndLength>[]
   xStart: number