react-msaview 3.1.12 → 3.2.1

package/dist/model.js.map

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

@@ -6,14 +6,14 @@ export function parseGFF(str) {
         .map(f => {
         const [seq_id, source, type, start, end, score, strand, phase, col9] = f.split('\t');
         return {
-            seq_id,
-            source,
-            type,
+            seq_id: seq_id,
+            source: source,
+            type: type,
             start: +start,
             end: +end,
             score: +score,
-            strand,
-            phase,
+            strand: strand,
+            phase: phase,
             ...Object.fromEntries(col9
                 .split(';')
                 .map(f => f.trim())
@@ -21,7 +21,9 @@ export function parseGFF(str) {
                 .map(f => f.split('='))
                 .map(([key, val]) => [
                 key.trim(),
-                decodeURIComponent(val).trim().split(',').join(' '),
+                val
+                    ? decodeURIComponent(val).trim().split(',').join(' ')
+                    : undefined,
             ])),
         };
     });

package/dist/parseGFF.js.map

@@ -1 +1 @@
-{"version":3,"file":"parseGFF.js","sourceRoot":"","sources":["../src/parseGFF.ts"],"names":[],"mappings":"AAAA,MAAM,UAAU,QAAQ,CAAC,GAAY;IACnC,OAAO,GAAG;QACR,EAAE,KAAK,CAAC,IAAI,CAAC;SACZ,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;SAClB,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,UAAU,CAAC,GAAG,CAAC,CAAC;SACtC,GAAG,CAAC,CAAC,CAAC,EAAE;QACP,MAAM,CAAC,MAAM,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,EAAE,GAAG,EAAE,KAAK,EAAE,MAAM,EAAE,KAAK,EAAE,IAAI,CAAC,GAClE,CAAC,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAEf,OAAO;YACL,MAAM;YACN,MAAM;YACN,IAAI;YACJ,KAAK,EAAE,CAAC,KAAK;YACb,GAAG,EAAE,CAAC,GAAG;YACT,KAAK,EAAE,CAAC,KAAK;YACb,MAAM;YACN,KAAK;YACL,GAAG,MAAM,CAAC,WAAW,CACnB,IAAI;iBACD,KAAK,CAAC,GAAG,CAAC;iBACV,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;iBAClB,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;iBAChB,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC;iBACtB,GAAG,CAAC,CAAC,CAAC,GAAG,EAAE,GAAG,CAAC,EAAE,EAAE,CAAC;gBACnB,GAAG,CAAC,IAAI,EAAE;gBACV,kBAAkB,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC;aACpD,CAAC,CACL;SACF,CAAA;IACH,CAAC,CAAC,CAAA;AACN,CAAC"}
+{"version":3,"file":"parseGFF.js","sourceRoot":"","sources":["../src/parseGFF.ts"],"names":[],"mappings":"AAAA,MAAM,UAAU,QAAQ,CAAC,GAAY;IACnC,OAAO,GAAG;QACR,EAAE,KAAK,CAAC,IAAI,CAAC;SACZ,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;SAClB,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,UAAU,CAAC,GAAG,CAAC,CAAC;SACtC,GAAG,CAAC,CAAC,CAAC,EAAE;QACP,MAAM,CAAC,MAAM,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,EAAE,GAAG,EAAE,KAAK,EAAE,MAAM,EAAE,KAAK,EAAE,IAAI,CAAC,GAClE,CAAC,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAEf,OAAO;YACL,MAAM,EAAE,MAAO;YACf,MAAM,EAAE,MAAO;YACf,IAAI,EAAE,IAAK;YACX,KAAK,EAAE,CAAC,KAAM;YACd,GAAG,EAAE,CAAC,GAAI;YACV,KAAK,EAAE,CAAC,KAAM;YACd,MAAM,EAAE,MAAO;YACf,KAAK,EAAE,KAAM;YACb,GAAG,MAAM,CAAC,WAAW,CACnB,IAAK;iBACF,KAAK,CAAC,GAAG,CAAC;iBACV,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;iBAClB,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;iBAChB,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC;iBACtB,GAAG,CAAC,CAAC,CAAC,GAAG,EAAE,GAAG,CAAC,EAAE,EAAE,CAAC;gBACnB,GAAI,CAAC,IAAI,EAAE;gBACX,GAAG;oBACD,CAAC,CAAC,kBAAkB,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC;oBACrD,CAAC,CAAC,SAAS;aACd,CAAC,CACL;SACF,CAAA;IACH,CAAC,CAAC,CAAA;AACN,CAAC"}

package/dist/parseNewick.js

@@ -59,7 +59,6 @@
  */
 export default function parse(s) {
     const ancestors = [];
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
     let tree = {};
     const tokens = s.split(/\s*(;|\(|\)|,|:)\s*/);
     for (let i = 0; i < tokens.length; i++) {
@@ -86,7 +85,7 @@ export default function parse(s) {
                     tree.name = token;
                 }
                 else if (x === ':') {
-                    tree.length = parseFloat(token);
+                    tree.length = Number.parseFloat(token);
                 }
             }
         }

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,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"}
+{"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"}

package/dist/parsers/ClustalMSA.d.ts

@@ -1,4 +1,4 @@
-import { NodeWithIds } from '../util';
+import type { NodeWithIds } from '../util';
 export default class ClustalMSA {
     private MSA;
     constructor(text: string);
@@ -13,7 +13,7 @@ export default class ClustalMSA {
             version: string;
         };
     };
-    getRow(name: string): any;
+    getRow(name: string): string;
     getWidth(): any;
     getRowData(): undefined;
     getHeader(): {

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,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"}

package/dist/parsers/FastaMSA.d.ts

@@ -1,4 +1,4 @@
-import { NodeWithIds } from '../util';
+import type { NodeWithIds } from '../util';
 export default class FastaMSA {
     private MSA;
     constructor(text: string);

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() {

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,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.d.ts

@@ -1,12 +1,12 @@
-import { NodeWithIds } from '../util';
+import { type NodeWithIds } from '../util';
 interface StockholmEntry {
     gf: {
         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],
         };
     }
@@ -64,7 +64,7 @@ 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))
             : {

package/dist/parsers/StockholmMSA.js.map

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

@@ -1,5 +1,5 @@
-import { Theme } from '@mui/material';
-import { MsaViewModel } from './model';
+import type { Theme } from '@mui/material';
+import type { MsaViewModel } from './model';
 export declare function renderToSvg(model: MsaViewModel, opts: {
     theme: Theme;
     includeMinimap?: boolean;

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';
@@ -8,7 +9,7 @@ import { colorContrast } from './util';
 import MinimapSVG from './components/minimap/MinimapSVG';
 import { renderBoxFeatureCanvasBlock } from './components/msa/renderBoxFeatureCanvasBlock';
 export async function renderToSvg(model, opts) {
-    await when(() => !!model.initialized);
+    await when(() => !!model.dataInitialized);
     const { width, height, scrollX, scrollY } = model;
     const { exportType, theme, includeMinimap } = opts;
     if (exportType === 'entire') {
@@ -22,7 +23,7 @@ export async function renderToSvg(model, opts) {
             includeMinimap,
         });
     }
-    else if (exportType === 'viewport') {
+    if (exportType === 'viewport') {
         return render({
             width,
             height,
@@ -33,9 +34,7 @@ export async function renderToSvg(model, opts) {
             includeMinimap,
         });
     }
-    else {
-        throw new Error('unknown export type');
-    }
+    throw new Error('unknown export type');
 }
 async function render({ width, height, offsetX, offsetY, theme, model, includeMinimap, }) {
     const { Context } = await import('svgcanvas');
@@ -86,12 +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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package/dist/reparseTree.d.ts

@@ -1,2 +1,2 @@
-import { NodeWithIds } from './util';
+import type { NodeWithIds } from './util';
 export declare function reparseTree(tree: NodeWithIds): NodeWithIds;

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

@@ -1,5 +1,5 @@
-import { HierarchyNode } from 'd3-hierarchy';
-import { Theme } from '@mui/material';
+import type { HierarchyNode } from 'd3-hierarchy';
+import type { Theme } from '@mui/material';
 export declare function transform<T>(obj: Record<string, T>, cb: (arg0: [string, T]) => [string, T]): {
     [k: string]: T;
 };

package/dist/util.js

@@ -54,8 +54,6 @@ export function collapse(d) {
         // @ts-expect-error
         d._children = d.children;
         // @ts-expect-error
-        d._children.forEach(collapse);
-        // @ts-expect-error
         d.children = null;
     }
 }

package/dist/util.js.map

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

@@ -1 +1 @@
-export declare const version = "3.1.12";
+export declare const version = "3.2.1";

package/dist/version.js

@@ -1,2 +1,2 @@
-export const version = '3.1.12';
+export const version = '3.2.1';
 //# sourceMappingURL=version.js.map

package/dist/version.js.map

@@ -1 +1 @@
-{"version":3,"file":"version.js","sourceRoot":"","sources":["../src/version.ts"],"names":[],"mappings":"AAAA,MAAM,CAAC,MAAM,OAAO,GAAG,QAAQ,CAAA"}
+{"version":3,"file":"version.js","sourceRoot":"","sources":["../src/version.ts"],"names":[],"mappings":"AAAA,MAAM,CAAC,MAAM,OAAO,GAAG,OAAO,CAAA"}

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "react-msaview",
   "author": "Colin",
-  "version": "3.1.12",
+  "version": "3.2.1",
   "license": "MIT",
   "main": "dist/index.js",
   "module": "dist/index.js",
@@ -15,6 +15,7 @@
   },
   "scripts": {
     "clean": "rimraf dist",
+    "format": "prettier --write .",
     "prebuild": "npm run clean",
     "prepublishOnly": "node output-version.js > src/version.ts && git add -A src && git commit -m '[skip ci] Bump version.ts'",
     "build:esm": "tsc",
@@ -22,8 +23,8 @@
     "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": {
     "@jbrowse/core": ">=2.0.0",
@@ -36,12 +37,18 @@
     "react-dom": ">=16.8.0"
   },
   "dependencies": {
+    "@eslint/js": "^9.8.0",
+    "@mui/icons-material": "^5.16.6",
+    "@mui/material": "^5.16.6",
+    "@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",
+    "eslint": "^9.8.0",
     "file-saver": "^2.0.5",
+    "pako": "^2.1.0",
     "rbush": "^3.0.1",
     "react-error-boundary": "^4.0.13",
     "stockholm-js": "^1.0.10",