react-msaview 3.1.2 → 3.1.4

package/dist/model.js

@@ -7,7 +7,7 @@ import { saveAs } from 'file-saver';
 // jbrowse
 import { FileLocation, ElementId } from '@jbrowse/core/util/types/mst';
 import { openLocation } from '@jbrowse/core/util/io';
-import { measureText, notEmpty, sum } from '@jbrowse/core/util';
+import { notEmpty, sum } from '@jbrowse/core/util';
 import BaseViewModel from '@jbrowse/core/pluggableElementTypes/models/BaseViewModel';
 // locals
 import { clamp, collapse, filterHiddenLeafNodes, generateNodeIds, maxLength, setBrLength, skipBlanks, } from './util';
@@ -23,6 +23,7 @@ import { StructureModel } from './StructureModel';
 import { DialogQueueSessionMixin } from './DialogQueue';
 import { renderToSvg } from './renderToSvg';
 import { blocksX, blocksY } from './calculateBlocks';
+import measureTextCanvas from './measureTextCanvas';
 /**
  * #stateModel MsaView
  * extends
@@ -230,13 +231,6 @@ const model = types
      * #volatile
      */
     error: undefined,
-    /**
-     * #volatile
-     */
-    margin: {
-        left: 20,
-        top: 20,
-    },
     /**
      * #volatile
      */
@@ -471,17 +465,15 @@ const model = types
      * #getter
      */
     get header() {
-        var _a;
-        return ((_a = this.MSA) === null || _a === void 0 ? void 0 : _a.getHeader()) || {};
+        return this.MSA?.getHeader() || {};
     },
     /**
      * #method
      */
     getRowData(name) {
-        var _a;
         const matches = name.match(/\S+\/(\d+)-(\d+)/);
         return {
-            data: ((_a = this.MSA) === null || _a === void 0 ? void 0 : _a.getRowData(name)) || {},
+            data: this.MSA?.getRowData(name) || {},
             ...(matches && {
                 range: {
                     start: +matches[1],
@@ -500,8 +492,7 @@ const model = types
      * #getter
      */
     get alignmentNames() {
-        var _a;
-        return ((_a = this.MSA) === null || _a === void 0 ? void 0 : _a.alignmentNames) || [];
+        return this.MSA?.alignmentNames || [];
     },
     /**
      * #getter
@@ -543,17 +534,15 @@ const model = types
      * #getter
      */
     get numColumns() {
-        var _a;
-        return (((_a = this.MSA) === null || _a === void 0 ? void 0 : _a.getWidth()) || 0) - this.blanks.length;
+        return (this.MSA?.getWidth() || 0) - this.blanks.length;
     },
     /**
      * #getter
      */
     get _tree() {
-        var _a;
         return self.data.tree
             ? generateNodeIds(parseNewick(self.data.tree))
-            : ((_a = this.MSA) === null || _a === void 0 ? void 0 : _a.getTree()) || {
+            : this.MSA?.getTree() || {
                 noTree: true,
                 branchset: [],
                 id: 'empty',
@@ -611,8 +600,7 @@ const model = types
      * #getter
      */
     get structures() {
-        var _a;
-        return ((_a = this.MSA) === null || _a === void 0 ? void 0 : _a.getStructures()) || {};
+        return this.MSA?.getStructures() || {};
     },
     /**
      * #getter
@@ -631,13 +619,12 @@ const model = types
      * #getter
      */
     get blanks() {
-        var _a;
         const blanks = [];
         const strs = this.hierarchy
             .leaves()
-            .map(leaf => { var _a; return (_a = this.MSA) === null || _a === void 0 ? void 0 : _a.getRow(leaf.data.name); })
+            .map(leaf => this.MSA?.getRow(leaf.data.name))
             .filter((item) => !!item);
-        for (let i = 0; i < ((_a = strs[0]) === null || _a === void 0 ? void 0 : _a.length); i++) {
+        for (let i = 0; i < strs[0]?.length; i++) {
             let counter = 0;
             for (const str of strs) {
                 if (str[i] === '-') {
@@ -657,7 +644,7 @@ const model = types
         const MSA = this.MSA;
         return this.hierarchy
             .leaves()
-            .map(leaf => [leaf.data.name, MSA === null || MSA === void 0 ? void 0 : MSA.getRow(leaf.data.name)])
+            .map(leaf => [leaf.data.name, MSA?.getRow(leaf.data.name)])
             .filter((f) => !!f[1]);
     },
     /**
@@ -824,11 +811,10 @@ const model = types
      * #action
      */
     setMouseoveredColumn(n, chain, file) {
-        var _a;
         let j = 0;
         let i = 0;
         const { id } = self.inverseStructures[file.slice(0, -4)] || {};
-        const row = (_a = self.MSA) === null || _a === void 0 ? void 0 : _a.getRow(id);
+        const row = self.MSA?.getRow(id);
         if (row) {
             for (i = 0; i < row.length && j < n; i++) {
                 if (row[i] !== '-') {
@@ -858,12 +844,11 @@ const model = types
      * #getter
      */
     get labelsWidth() {
-        var _a;
         let x = 0;
         const { rowHeight, hierarchy, treeMetadata, fontSize } = self;
         if (rowHeight > 5) {
             for (const node of hierarchy.leaves()) {
-                x = Math.max(measureText(((_a = treeMetadata[node.data.name]) === null || _a === void 0 ? void 0 : _a.genome) || node.data.name, fontSize), x);
+                x = Math.max(measureTextCanvas(treeMetadata[node.data.name]?.genome || node.data.name, fontSize), x);
             }
         }
         return x;
@@ -872,15 +857,13 @@ const model = types
      * #getter
      */
     get secondaryStructureConsensus() {
-        var _a;
-        return (_a = self.MSA) === null || _a === void 0 ? void 0 : _a.secondaryStructureConsensus;
+        return self.MSA?.secondaryStructureConsensus;
     },
     /**
      * #getter
      */
     get seqConsensus() {
-        var _a;
-        return (_a = self.MSA) === null || _a === void 0 ? void 0 : _a.seqConsensus;
+        return self.MSA?.seqConsensus;
     },
     /**
      * #getter
@@ -900,15 +883,14 @@ const model = types
      * #getter
      */
     get adapterTrackModels() {
-        var _a;
-        return (((_a = self.MSA) === null || _a === void 0 ? void 0 : _a.tracks.map(t => ({
+        return (self.MSA?.tracks.map(t => ({
             model: {
                 ...t,
                 data: t.data ? skipBlanks(self.blanks, t.data) : undefined,
                 height: self.rowHeight,
             },
             ReactComponent: TextTrack,
-        }))) || []);
+        })) || []);
     },
     /**
      * #getter
@@ -944,12 +926,11 @@ const model = types
      * #method
      */
     rowSpecificBpToPx(rowName, position) {
-        var _a;
         const { rowNames, rows } = self;
         const index = rowNames.indexOf(rowName);
         const row = rows[index][1];
         const details = self.getRowData(rowName);
-        const offset = ((_a = details.range) === null || _a === void 0 ? void 0 : _a.start) || 0;
+        const offset = details.range?.start || 0;
         const current = position - offset;
         const s = new Set(self.blanks);
         if (current < 0) {
@@ -974,10 +955,9 @@ const model = types
      * #method
      */
     globalBpToPx(position) {
-        var _a;
         let count = 0;
         const s = new Set(self.blanks);
-        for (let k = 0; k < ((_a = self.rows[0]) === null || _a === void 0 ? void 0 : _a[1].length); k++) {
+        for (let k = 0; k < self.rows[0]?.[1].length; k++) {
             if (s.has(k) && k < position + 1) {
                 count++;
             }
@@ -1109,7 +1089,7 @@ const model = types
         // autorun synchronizes treeWidth with treeAreaWidth
         addDisposer(self, autorun(async () => {
             if (self.treeWidthMatchesArea) {
-                self.setTreeWidth(Math.max(50, self.treeAreaWidth - self.labelsWidth - 20));
+                self.setTreeWidth(Math.max(50, self.treeAreaWidth - self.labelsWidth - 10));
             }
         }));
     },

package/dist/model.js.map

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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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package/dist/renderToSvg.d.ts

@@ -3,4 +3,5 @@ import { MsaViewModel } from './model';
 export declare function renderToSvg(model: MsaViewModel, opts: {
     theme: Theme;
     includeMinimap?: boolean;
+    exportType: string;
 }): Promise<string>;