msa-parsers 5.0.7 → 5.0.13

package/dist/msa/StockholmMSA.d.ts

@@ -1,6 +1,7 @@
+import BaseMSA from './BaseMSA.ts';
 import type { NodeWithIds } from '../types.ts';
 import type { StockholmData } from './stockholmParser.ts';
-export default class StockholmMSA {
+export default class StockholmMSA extends BaseMSA {
     private data;
     private MSA;
     constructor(text: string, currentAlignment: number);
@@ -23,7 +24,6 @@ export default class StockholmMSA {
         dbxref: string | undefined;
     };
     getNames(): string[];
-    getSeqCoords(): void;
     getStructures(): Record<string, {
         pdb: string;
         chain: string;

package/dist/msa/StockholmMSA.js

@@ -1,10 +1,12 @@
 import parseNewick from "./parseNewick.js";
 import { parseAll } from "./stockholmParser.js";
 import { generateNodeIds } from "../util.js";
-export default class StockholmMSA {
+import BaseMSA from "./BaseMSA.js";
+export default class StockholmMSA extends BaseMSA {
     data;
     MSA;
     constructor(text, currentAlignment) {
+        super();
         const res = parseAll(text);
         this.data = res;
         this.MSA = res[currentAlignment];
@@ -41,47 +43,29 @@ export default class StockholmMSA {
     getNames() {
         return Object.keys(this.MSA.seqdata);
     }
-    getSeqCoords() { }
     getStructures() {
         const pdbRegex = /PDB; +(\S+) +(\S); ([0-9]+)-([0-9]+)/;
         const drEntries = this.MSA.gs.DR ?? {};
-        const args = Object.entries(drEntries)
-            .flatMap(([id, drList]) => drList.map(dr => {
-            const match = pdbRegex.exec(dr);
-            return match ? { id, match } : null;
-        }))
-            .filter((item) => !!item)
-            .map(({ id, match }) => ({
-            id,
-            pdb: match[1].toLowerCase(),
-            chain: match[2],
-            startPos: +match[3],
-            endPos: +match[4],
-        }));
-        const ret = {};
-        for (const entry of args) {
-            const { id, ...rest } = entry;
-            if (!ret[id]) {
-                ret[id] = [];
+        const result = {};
+        for (const [id, drList] of Object.entries(drEntries)) {
+            for (const dr of drList) {
+                const match = pdbRegex.exec(dr);
+                if (match) {
+                    ;
+                    (result[id] ??= []).push({
+                        pdb: match[1].toLowerCase(),
+                        chain: match[2],
+                        startPos: +match[3],
+                        endPos: +match[4],
+                    });
+                }
             }
-            ret[id].push(rest);
         }
-        return ret;
+        return result;
     }
     getTree() {
         const tree = this.MSA.gf.NH?.[0];
-        return tree
-            ? generateNodeIds(parseNewick(tree))
-            : {
-                id: 'root',
-                name: 'root',
-                noTree: true,
-                children: this.getNames().map(name => ({
-                    id: name,
-                    children: [],
-                    name,
-                })),
-            };
+        return tree ? generateNodeIds(parseNewick(tree)) : super.getTree();
     }
     get seqConsensus() {
         return this.MSA.gc.seq_cons;

package/dist/msa/StockholmMSA.js.map

@@ -1 +1 @@
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+{"version":3,"file":"StockholmMSA.js","sourceRoot":"","sources":["../../src/msa/StockholmMSA.ts"],"names":[],"mappings":"AAAA,OAAO,WAAW,MAAM,kBAAkB,CAAA;AAC1C,OAAO,EAAE,QAAQ,EAAE,MAAM,sBAAsB,CAAA;AAC/C,OAAO,EAAE,eAAe,EAAE,MAAM,YAAY,CAAA;AAC5C,OAAO,OAAO,MAAM,cAAc,CAAA;AAKlC,MAAM,CAAC,OAAO,OAAO,YAAa,SAAQ,OAAO;IACvC,IAAI,CAAiB;IACrB,GAAG,CAAe;IAE1B,YAAY,IAAY,EAAE,gBAAwB;QAChD,KAAK,EAAE,CAAA;QACP,MAAM,GAAG,GAAG,QAAQ,CAAC,IAAI,CAAC,CAAA;QAC1B,IAAI,CAAC,IAAI,GAAG,GAAG,CAAA;QACf,IAAI,CAAC,GAAG,GAAG,GAAG,CAAC,gBAAgB,CAAE,CAAA;IACnC,CAAC;IAED,MAAM;QACJ,OAAO,IAAI,CAAC,GAAG,CAAA;IACjB,CAAC;IAED,MAAM,CAAC,IAAY;QACjB,OAAO,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,IAAI,CAAC,IAAI,EAAE,CAAA;IACrC,CAAC;IAED,QAAQ;QACN,MAAM,IAAI,GAAG,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,CAAE,CAAA;QAC9C,OAAO,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,MAAM,CAAA;IACjC,CAAC;IAED,IAAI,cAAc;QAChB,OAAO,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,GAAG,EAAE,GAAG,EAAE,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,aAAa,GAAG,GAAG,CAAC,EAAE,CAAC,CAAA;IAC9E,CAAC;IAED,SAAS;QACP,MAAM,SAAS,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,IAAI,EAAE,CAAA;QACtC,MAAM,SAAS,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,IAAI,EAAE,CAAA;QACtC,OAAO;YACL,OAAO,EAAE,IAAI,CAAC,GAAG,CAAC,EAAE;YACpB,UAAU,EAAE,MAAM,CAAC,WAAW,CAC5B,MAAM,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CACrD;YACD,MAAM,EAAE,MAAM,CAAC,WAAW,CACxB,MAAM,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,CAC7D;SACF,CAAA;IACH,CAAC;IAED,UAAU,CAAC,OAAe;QACxB,OAAO;YACL,IAAI,EAAE,OAAO;YACb,SAAS,EAAE,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC;YACzC,MAAM,EAAE,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,OAAO,CAAC,EAAE,IAAI,CAAC,IAAI,CAAC;SAC9C,CAAA;IACH,CAAC;IAED,QAAQ;QACN,OAAO,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;IACtC,CAAC;IAED,aAAa;QACX,MAAM,QAAQ,GAAG,sCAAsC,CAAA;QACvD,MAAM,SAAS,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,IAAI,EAAE,CAAA;QACtC,MAAM,MAAM,GAGR,EAAE,CAAA;QACN,KAAK,MAAM,CAAC,EAAE,EAAE,MAAM,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,SAAS,CAAC,EAAE,CAAC;YACrD,KAAK,MAAM,EAAE,IAAI,MAAM,EAAE,CAAC;gBACxB,MAAM,KAAK,GAAG,QAAQ,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;gBAC/B,IAAI,KAAK,EAAE,CAAC;oBACV,CAAC;oBAAA,CAAC,MAAM,CAAC,EAAE,CAAC,KAAK,EAAE,CAAC,CAAC,IAAI,CAAC;wBACxB,GAAG,EAAE,KAAK,CAAC,CAAC,CAAE,CAAC,WAAW,EAAE;wBAC5B,KAAK,EAAE,KAAK,CAAC,CAAC,CAAE;wBAChB,QAAQ,EAAE,CAAC,KAAK,CAAC,CAAC,CAAE;wBACpB,MAAM,EAAE,CAAC,KAAK,CAAC,CAAC,CAAE;qBACnB,CAAC,CAAA;gBACJ,CAAC;YACH,CAAC;QACH,CAAC;QACD,OAAO,MAAM,CAAA;IACf,CAAC;IAED,OAAO;QACL,MAAM,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAA;QAChC,OAAO,IAAI,CAAC,CAAC,CAAC,eAAe,CAAC,WAAW,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,EAAE,CAAA;IACpE,CAAC;IAED,IAAI,YAAY;QACd,OAAO,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,QAAQ,CAAA;IAC7B,CAAC;IAED,IAAI,2BAA2B;QAC7B,OAAO,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,OAAO,CAAA;IAC5B,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;AAED,OAAO,EAAE,KAAK,IAAI,cAAc,EAAE,MAAM,sBAAsB,CAAA"}

package/package.json

@@ -1,8 +1,13 @@
 {
   "name": "msa-parsers",
-  "version": "5.0.7",
+  "version": "5.0.13",
   "license": "MIT",
   "type": "module",
+  "repository": {
+    "type": "git",
+    "url": "https://github.com/GMOD/JBrowseMSA.git",
+    "directory": "packages/msa-parsers"
+  },
   "exports": {
     ".": {
       "types": "./dist/index.d.ts",
@@ -23,7 +28,7 @@
   },
   "devDependencies": {
     "typescript": "^6.0.2",
-    "vitest": "^4.1.1"
+    "vitest": "^4.1.4"
   },
   "scripts": {
     "clean": "rimraf dist",

package/src/gff/gffToInterPro.ts

@@ -89,17 +89,6 @@ export function gffToInterProResults(
   return results
 }
 
-/**
- * Convert GFF string directly to InterProScan format
- */
-export function parseGFFToInterPro(
-  gffStr: string,
-  parseGFFfn: (str: string) => GFFRecord[],
-): Record<string, InterProScanResults> {
-  const records = parseGFFfn(gffStr)
-  return gffToInterProResults(records)
-}
-
 /**
  * Create a full InterProScanResponse from GFF records
  */

package/src/msa/A3mMSA.ts

@@ -1,4 +1,4 @@
-import type { NodeWithIds } from '../types.ts'
+import BaseMSA from './BaseMSA.ts'
 
 /**
  * A3M Format Parser
@@ -22,7 +22,6 @@ import type { NodeWithIds } from '../types.ts'
  * @see https://yanglab.qd.sdu.edu.cn/trRosetta/msa_format.html
  */
 
-// Char code helpers for fast character classification
 const CODE_A = 65 // 'A'
 const CODE_Z = 90 // 'Z'
 const CODE_a = 97 // 'a'
@@ -34,15 +33,15 @@ function isLower(code: number): boolean {
   return code >= CODE_a && code <= CODE_z
 }
 
-export default class A3mMSA {
+export default class A3mMSA extends BaseMSA {
   private MSA: { seqdata: Record<string, string> }
   private orderedNames: string[]
 
   constructor(text: string) {
+    super()
     const rawSeqs: string[] = []
     const names: string[] = []
 
-    // First pass: parse sequences (like FASTA), preserving order
     for (const entry of text.split('>')) {
       if (!/\S/.test(entry)) {
         continue
@@ -64,9 +63,6 @@ export default class A3mMSA {
     this.MSA = { seqdata: this.expandA3M(rawSeqs, names) }
   }
 
-  /**
-   * Detect if text is likely A3M format
-   */
   static sniff(text: string): boolean {
     if (!text.startsWith('>')) {
       return false
@@ -91,8 +87,6 @@ export default class A3mMSA {
       return false
     }
 
-    // Check for lowercase and compute match column lengths in single pass per sequence
-    // In A3M, match columns = uppercase letters + dashes (deletions)
     let hasLowercase = false
     let firstMatchLen = -1
     let sameMatchLength = true
@@ -104,7 +98,6 @@ export default class A3mMSA {
         if (isLower(code)) {
           hasLowercase = true
         } else if ((code >= CODE_A && code <= CODE_Z) || code === CODE_DASH) {
-          // Uppercase letters and dashes are match columns
           matchLen++
         }
       }
@@ -121,14 +114,6 @@ export default class A3mMSA {
     return hasLowercase && sameMatchLength
   }
 
-  /**
-   * Expand A3M format to standard aligned format.
-   *
-   * In A3M, lowercase characters are insertions that implicitly introduce
-   * gaps in sequences that don't have an insert at that position.
-   * Gaps (-) following match columns in sequences without inserts align
-   * with lowercase inserts in other sequences.
-   */
   private expandA3M(
     rawSeqs: string[],
     names: string[],
@@ -138,8 +123,6 @@ export default class A3mMSA {
       return {}
     }
 
-    // Parse sequences: extract match chars (uppercase only) and insert content
-    // For each sequence, track: matchChars, insertContent (after each match)
     const matchChars: string[][] = []
     const insertContent: string[][] = []
 
@@ -153,10 +136,7 @@ export default class A3mMSA {
         const code = seq.charCodeAt(i)
 
         if ((code >= CODE_A && code <= CODE_Z) || code === CODE_DASH) {
-          // Uppercase letter or dash - match column (dash = deletion)
           matches.push(seq[i]!)
-          // Collect following lowercase/dot characters as insert content
-          // Note: dash is NOT insert content, it's a match column
           let ins = ''
           let j = i + 1
           while (j < seq.length) {
@@ -171,16 +151,13 @@ export default class A3mMSA {
           inserts.push(ins)
           i = j
         } else if (code === CODE_DOT) {
-          // Leading dot (gap aligned to insert) - skip
           i++
         } else if (isLower(code)) {
-          // Leading insert before first match
           let ins = ''
           while (i < seq.length && isLower(seq.charCodeAt(i))) {
             ins += seq[i]!
             i++
           }
-          // Add empty match with this insert
           matches.push('')
           inserts.push(ins)
         } else {
@@ -192,15 +169,12 @@ export default class A3mMSA {
       insertContent.push(inserts)
     }
 
-    // Find number of match positions (should be same for all valid A3M)
     const numPositions = Math.max(...matchChars.map(m => m.length), 0)
 
-    // Find max insert length at each position (only count lowercase, not gaps)
     const maxInserts = new Array<number>(numPositions).fill(0)
     for (let seqIdx = 0; seqIdx < numSeqs; seqIdx++) {
       const inserts = insertContent[seqIdx]!
       for (let pos = 0; pos < inserts.length; pos++) {
-        // Count only lowercase characters as actual inserts
         let lcCount = 0
         for (const c of inserts[pos]!) {
           if (isLower(c.charCodeAt(0))) {
@@ -213,7 +187,6 @@ export default class A3mMSA {
       }
     }
 
-    // Build expanded sequences
     const expanded: Record<string, string> = {}
 
     for (let seqIdx = 0; seqIdx < numSeqs; seqIdx++) {
@@ -228,10 +201,8 @@ export default class A3mMSA {
           const matchChar = matches[pos]!
           const insContent = inserts[pos] || ''
 
-          // Add match character (or gap if empty)
           result.push(matchChar || '-')
 
-          // Process insert content
           let lcContent = ''
           for (const c of insContent) {
             if (isLower(c.charCodeAt(0))) {
@@ -239,16 +210,13 @@ export default class A3mMSA {
             }
           }
 
-          // Add the insert content (uppercased)
           result.push(lcContent)
 
-          // Pad with gaps to match max insert length
           const padding = maxIns - lcContent.length
           if (padding > 0) {
             result.push('.'.repeat(padding))
           }
         } else {
-          // This sequence is shorter - add gaps
           result.push('-')
           if (maxIns > 0) {
             result.push('.'.repeat(maxIns))
@@ -266,10 +234,6 @@ export default class A3mMSA {
     return this.MSA
   }
 
-  getRowData() {
-    return undefined
-  }
-
   getNames() {
     return this.orderedNames
   }
@@ -282,41 +246,4 @@ export default class A3mMSA {
     const name = Object.keys(this.MSA.seqdata)[0]
     return name ? this.getRow(name).length : 0
   }
-
-  getStructures() {
-    return {}
-  }
-
-  get alignmentNames() {
-    return []
-  }
-
-  getHeader() {
-    return {}
-  }
-
-  getTree(): NodeWithIds {
-    return {
-      id: 'root',
-      name: 'root',
-      noTree: true,
-      children: this.getNames().map(name => ({
-        id: name,
-        children: [],
-        name,
-      })),
-    }
-  }
-
-  get seqConsensus() {
-    return undefined
-  }
-
-  get secondaryStructureConsensus() {
-    return undefined
-  }
-
-  get tracks() {
-    return []
-  }
 }

package/src/msa/BaseMSA.ts

@@ -0,0 +1,49 @@
+import type { NodeWithIds } from '../types.ts'
+
+export default abstract class BaseMSA {
+  abstract getMSA(): unknown
+  abstract getRow(name: string): string
+  abstract getWidth(): number
+  abstract getNames(): string[]
+
+  getTree(): NodeWithIds {
+    return {
+      id: 'root',
+      name: 'root',
+      noTree: true,
+      children: this.getNames().map(name => ({
+        id: name,
+        children: [],
+        name,
+      })),
+    }
+  }
+
+  getRowData(_name: string) {
+    return undefined as { name?: string; accession?: string; dbxref?: string } | undefined
+  }
+
+  getStructures(): Record<string, unknown> {
+    return {}
+  }
+
+  getHeader(): unknown {
+    return {}
+  }
+
+  get alignmentNames(): string[] {
+    return []
+  }
+
+  get seqConsensus(): string | undefined {
+    return undefined
+  }
+
+  get secondaryStructureConsensus(): string | undefined {
+    return undefined
+  }
+
+  get tracks(): unknown[] {
+    return []
+  }
+}

package/src/msa/ClustalMSA.ts

@@ -1,11 +1,12 @@
 import { parse } from 'clustal-js'
 
-import type { NodeWithIds } from '../types.ts'
+import BaseMSA from './BaseMSA.ts'
 
-export default class ClustalMSA {
+export default class ClustalMSA extends BaseMSA {
   private MSA: ReturnType<typeof parse>
 
   constructor(text: string) {
+    super()
     this.MSA = parse(text)
   }
 
@@ -21,10 +22,6 @@ export default class ClustalMSA {
     return this.MSA.alns[0]!.seq.length
   }
 
-  getRowData() {
-    return undefined
-  }
-
   getHeader() {
     return this.MSA.header
   }
@@ -33,35 +30,7 @@ export default class ClustalMSA {
     return this.MSA.alns.map(aln => aln.id)
   }
 
-  getStructures() {
-    return {}
-  }
-
-  get alignmentNames() {
-    return []
-  }
-
-  getTree(): NodeWithIds {
-    return {
-      id: 'root',
-      name: 'root',
-      noTree: true,
-      children: this.getNames().map(name => ({
-        id: name,
-        name,
-        children: [],
-      })),
-    }
-  }
-
   get seqConsensus() {
     return this.MSA.consensus
   }
-  get secondaryStructureConsensus() {
-    return undefined
-  }
-
-  get tracks() {
-    return []
-  }
 }

package/src/msa/EmfMSA.ts

@@ -1,11 +1,12 @@
 import { parseEmfAln } from 'emf-js'
 
-import type { NodeWithIds } from '../types.ts'
+import BaseMSA from './BaseMSA.ts'
 
-export default class EmfMSA {
+export default class EmfMSA extends BaseMSA {
   private MSA: ReturnType<typeof parseEmfAln>
 
   constructor(text: string) {
+    super()
     this.MSA = parseEmfAln(text)
   }
 
@@ -21,10 +22,6 @@ export default class EmfMSA {
     return this.MSA[0]!.seq.length
   }
 
-  getRowData() {
-    return undefined
-  }
-
   getHeader() {
     return ''
   }
@@ -32,36 +29,4 @@ export default class EmfMSA {
   getNames() {
     return this.MSA.map(aln => aln.protein)
   }
-
-  getStructures() {
-    return {}
-  }
-
-  get alignmentNames() {
-    return []
-  }
-
-  getTree(): NodeWithIds {
-    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 []
-  }
 }

package/src/msa/FastaMSA.ts

@@ -1,12 +1,13 @@
-import type { NodeWithIds } from '../types.ts'
+import BaseMSA from './BaseMSA.ts'
 
-export default class FastaMSA {
+export default class FastaMSA extends BaseMSA {
   private MSA: {
     seqdata: Record<string, string>
     colonNormalized: Record<string, string>
   }
 
   constructor(text: string) {
+    super()
     const seqdata: Record<string, string> = {}
     const colonNormalized: Record<string, string> = {}
     for (const entry of text.split('>')) {
@@ -34,10 +35,6 @@ export default class FastaMSA {
     return this.MSA
   }
 
-  getRowData() {
-    return undefined
-  }
-
   getNames() {
     return Object.keys(this.MSA.seqdata)
   }
@@ -54,40 +51,4 @@ export default class FastaMSA {
     const name = Object.keys(this.MSA.seqdata)[0]!
     return this.getRow(name).length
   }
-
-  getStructures() {
-    return {}
-  }
-
-  get alignmentNames() {
-    return []
-  }
-
-  getHeader() {
-    return {}
-  }
-
-  getTree(): NodeWithIds {
-    return {
-      id: 'root',
-      name: 'root',
-      noTree: true,
-      children: this.getNames().map(name => ({
-        id: name,
-        children: [],
-        name,
-      })),
-    }
-  }
-
-  get seqConsensus() {
-    return undefined
-  }
-  get secondaryStructureConsensus() {
-    return undefined
-  }
-
-  get tracks() {
-    return []
-  }
 }

package/src/msa/StockholmMSA.ts

@@ -1,15 +1,17 @@
 import parseNewick from './parseNewick.ts'
 import { parseAll } from './stockholmParser.ts'
 import { generateNodeIds } from '../util.ts'
+import BaseMSA from './BaseMSA.ts'
 
 import type { NodeWithIds } from '../types.ts'
 import type { StockholmData } from './stockholmParser.ts'
 
-export default class StockholmMSA {
+export default class StockholmMSA extends BaseMSA {
   private data: StockholmData[]
   private MSA: StockholmData
 
   constructor(text: string, currentAlignment: number) {
+    super()
     const res = parseAll(text)
     this.data = res
     this.MSA = res[currentAlignment]!
@@ -58,55 +60,32 @@ export default class StockholmMSA {
     return Object.keys(this.MSA.seqdata)
   }
 
-  getSeqCoords() {}
-
   getStructures() {
     const pdbRegex = /PDB; +(\S+) +(\S); ([0-9]+)-([0-9]+)/
     const drEntries = this.MSA.gs.DR ?? {}
-    const args = Object.entries(drEntries)
-      .flatMap(([id, drList]) =>
-        drList.map(dr => {
-          const match = pdbRegex.exec(dr)
-          return match ? { id, match } : null
-        }),
-      )
-      .filter((item): item is { id: string; match: RegExpExecArray } => !!item)
-      .map(({ id, match }) => ({
-        id,
-        pdb: match[1]!.toLowerCase(),
-        chain: match[2]!,
-        startPos: +match[3]!,
-        endPos: +match[4]!,
-      }))
-
-    const ret = {} as Record<
+    const result: Record<
       string,
       { pdb: string; chain: string; startPos: number; endPos: number }[]
-    >
-    for (const entry of args) {
-      const { id, ...rest } = entry
-      if (!ret[id]) {
-        ret[id] = []
+    > = {}
+    for (const [id, drList] of Object.entries(drEntries)) {
+      for (const dr of drList) {
+        const match = pdbRegex.exec(dr)
+        if (match) {
+          ;(result[id] ??= []).push({
+            pdb: match[1]!.toLowerCase(),
+            chain: match[2]!,
+            startPos: +match[3]!,
+            endPos: +match[4]!,
+          })
+        }
       }
-      ret[id].push(rest)
     }
-    return ret
+    return result
   }
 
   getTree(): NodeWithIds {
     const tree = this.MSA.gf.NH?.[0]
-    return tree
-      ? generateNodeIds(parseNewick(tree))
-      : {
-          id: 'root',
-          name: 'root',
-          noTree: true,
-          children: this.getNames().map(name => ({
-            id: name,
-            children: [],
-            name,
-          })),
-        }
+    return tree ? generateNodeIds(parseNewick(tree)) : super.getTree()
   }
 
   get seqConsensus() {