msa-parsers 5.0.7 → 5.0.13

package/dist/gff/gffToInterPro.d.ts

@@ -10,10 +10,6 @@ import type { GFFRecord, InterProScanResponse, InterProScanResults } from '../ty
  * - Attributes: Name (accession), signature_desc (name), Dbxref, etc.
  */
 export declare function gffToInterProResults(gffRecords: GFFRecord[]): Record<string, InterProScanResults>;
-/**
- * Convert GFF string directly to InterProScan format
- */
-export declare function parseGFFToInterPro(gffStr: string, parseGFFfn: (str: string) => GFFRecord[]): Record<string, InterProScanResults>;
 /**
  * Create a full InterProScanResponse from GFF records
  */

package/dist/gff/gffToInterPro.js

@@ -64,13 +64,6 @@ export function gffToInterProResults(gffRecords) {
     }
     return results;
 }
-/**
- * Convert GFF string directly to InterProScan format
- */
-export function parseGFFToInterPro(gffStr, parseGFFfn) {
-    const records = parseGFFfn(gffStr);
-    return gffToInterProResults(records);
-}
 /**
  * Create a full InterProScanResponse from GFF records
  */

package/dist/gff/gffToInterPro.js.map

@@ -1 +1 @@
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+{"version":3,"file":"gffToInterPro.js","sourceRoot":"","sources":["../../src/gff/gffToInterPro.ts"],"names":[],"mappings":"AAMA;;;;;;;;;GASG;AACH,MAAM,UAAU,oBAAoB,CAClC,UAAuB;IAEvB,MAAM,UAAU,GAAG,IAAI,GAAG,EAAuB,CAAA;IAEjD,KAAK,MAAM,MAAM,IAAI,UAAU,EAAE,CAAC;QAChC,MAAM,QAAQ,GAAG,UAAU,CAAC,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;QAC9C,IAAI,QAAQ,EAAE,CAAC;YACb,QAAQ,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA;QACvB,CAAC;aAAM,CAAC;YACN,UAAU,CAAC,GAAG,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,MAAM,CAAC,CAAC,CAAA;QACzC,CAAC;IACH,CAAC;IAED,MAAM,OAAO,GAAwC,EAAE,CAAA;IAEvD,KAAK,MAAM,CAAC,KAAK,EAAE,OAAO,CAAC,IAAI,UAAU,EAAE,CAAC;QAC1C,MAAM,kBAAkB,GAAG,IAAI,GAAG,EAG/B,CAAA;QACH,MAAM,SAAS,GAAG,IAAI,GAAG,EAGtB,CAAA;QAEH,KAAK,MAAM,MAAM,IAAI,OAAO,EAAE,CAAC;YAC7B,MAAM,SAAS,GACZ,MAAM,CAAC,IAAe;gBACtB,MAAM,CAAC,EAAa;gBACrB,GAAG,MAAM,CAAC,MAAM,IAAI,MAAM,CAAC,KAAK,IAAI,MAAM,CAAC,GAAG,EAAE,CAAA;YAClD,MAAM,IAAI,GACP,MAAM,CAAC,cAAyB;gBAChC,MAAM,CAAC,IAAe;gBACvB,SAAS,CAAA;YACX,MAAM,WAAW,GACd,MAAM,CAAC,aAAwB;gBAC/B,MAAM,CAAC,WAAsB;gBAC7B,MAAM,CAAC,IAAe;gBACvB,IAAI,CAAA;YAEN,IAAI,CAAC,SAAS,CAAC,GAAG,CAAC,SAAS,CAAC,EAAE,CAAC;gBAC9B,SAAS,CAAC,GAAG,CAAC,SAAS,EAAE,EAAE,IAAI,EAAE,WAAW,EAAE,SAAS,EAAE,CAAC,CAAA;YAC5D,CAAC;YAED,MAAM,SAAS,GAAG,kBAAkB,CAAC,GAAG,CAAC,SAAS,CAAC,CAAA;YACnD,IAAI,SAAS,EAAE,CAAC;gBACd,SAAS,CAAC,IAAI,CAAC,EAAE,KAAK,EAAE,MAAM,CAAC,KAAK,EAAE,GAAG,EAAE,MAAM,CAAC,GAAG,EAAE,CAAC,CAAA;YAC1D,CAAC;iBAAM,CAAC;gBACN,kBAAkB,CAAC,GAAG,CAAC,SAAS,EAAE;oBAChC,EAAE,KAAK,EAAE,MAAM,CAAC,KAAK,EAAE,GAAG,EAAE,MAAM,CAAC,GAAG,EAAE;iBACzC,CAAC,CAAA;YACJ,CAAC;QACH,CAAC;QAED,MAAM,OAAO,GAAG,EAAE,CAAA;QAClB,KAAK,MAAM,CAAC,SAAS,EAAE,SAAS,CAAC,IAAI,kBAAkB,EAAE,CAAC;YACxD,MAAM,IAAI,GAAG,SAAS,CAAC,GAAG,CAAC,SAAS,CAAE,CAAA;YACtC,OAAO,CAAC,IAAI,CAAC;gBACX,SAAS,EAAE;oBACT,KAAK,EAAE,IAAI;iBACZ;gBACD,SAAS;aACV,CAAC,CAAA;QACJ,CAAC;QAED,OAAO,CAAC,KAAK,CAAC,GAAG;YACf,OAAO;YACP,IAAI,EAAE,CAAC,EAAE,EAAE,EAAE,KAAK,EAAE,CAAC;SACtB,CAAA;IACH,CAAC;IAED,OAAO,OAAO,CAAA;AAChB,CAAC;AAED;;GAEG;AACH,MAAM,UAAU,qBAAqB,CACnC,UAAuB;IAEvB,MAAM,UAAU,GAAG,oBAAoB,CAAC,UAAU,CAAC,CAAA;IACnD,OAAO;QACL,OAAO,EAAE,MAAM,CAAC,MAAM,CAAC,UAAU,CAAC;KACnC,CAAA;AACH,CAAC"}

package/dist/msa/A3mMSA.d.ts

@@ -1,33 +1,14 @@
-import type { NodeWithIds } from '../types.ts';
-export default class A3mMSA {
+import BaseMSA from './BaseMSA.ts';
+export default class A3mMSA extends BaseMSA {
     private MSA;
     private orderedNames;
     constructor(text: string);
-    /**
-     * Detect if text is likely A3M format
-     */
     static sniff(text: string): boolean;
-    /**
-     * 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;
     getMSA(): {
         seqdata: Record<string, string>;
     };
-    getRowData(): undefined;
     getNames(): string[];
     getRow(name: string): string;
     getWidth(): number;
-    getStructures(): {};
-    get alignmentNames(): never[];
-    getHeader(): {};
-    getTree(): NodeWithIds;
-    get seqConsensus(): undefined;
-    get secondaryStructureConsensus(): undefined;
-    get tracks(): never[];
 }

package/dist/msa/A3mMSA.js

@@ -1,3 +1,4 @@
+import BaseMSA from "./BaseMSA.js";
 /**
  * A3M Format Parser
  *
@@ -19,7 +20,6 @@
  *
  * @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'
@@ -29,13 +29,13 @@ const CODE_DOT = 46; // '.'
 function isLower(code) {
     return code >= CODE_a && code <= CODE_z;
 }
-export default class A3mMSA {
+export default class A3mMSA extends BaseMSA {
     MSA;
     orderedNames;
     constructor(text) {
+        super();
         const rawSeqs = [];
         const names = [];
-        // First pass: parse sequences (like FASTA), preserving order
         for (const entry of text.split('>')) {
             if (!/\S/.test(entry)) {
                 continue;
@@ -55,9 +55,6 @@ export default class A3mMSA {
         this.orderedNames = names;
         this.MSA = { seqdata: this.expandA3M(rawSeqs, names) };
     }
-    /**
-     * Detect if text is likely A3M format
-     */
     static sniff(text) {
         if (!text.startsWith('>')) {
             return false;
@@ -79,8 +76,6 @@ export default class A3mMSA {
         if (seqs.length < 2) {
             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;
@@ -92,7 +87,6 @@ export default class A3mMSA {
                     hasLowercase = true;
                 }
                 else if ((code >= CODE_A && code <= CODE_Z) || code === CODE_DASH) {
-                    // Uppercase letters and dashes are match columns
                     matchLen++;
                 }
             }
@@ -107,21 +101,11 @@ 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.
-     */
     expandA3M(rawSeqs, names) {
         const numSeqs = names.length;
         if (numSeqs === 0) {
             return {};
         }
-        // Parse sequences: extract match chars (uppercase only) and insert content
-        // For each sequence, track: matchChars, insertContent (after each match)
         const matchChars = [];
         const insertContent = [];
         for (let seqIdx = 0; seqIdx < numSeqs; seqIdx++) {
@@ -132,10 +116,7 @@ export default class A3mMSA {
             while (i < seq.length) {
                 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) {
@@ -152,17 +133,14 @@ export default class A3mMSA {
                     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);
                 }
@@ -173,14 +151,11 @@ export default class A3mMSA {
             matchChars.push(matches);
             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(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))) {
@@ -192,7 +167,6 @@ export default class A3mMSA {
                 }
             }
         }
-        // Build expanded sequences
         const expanded = {};
         for (let seqIdx = 0; seqIdx < numSeqs; seqIdx++) {
             const matches = matchChars[seqIdx];
@@ -203,25 +177,20 @@ export default class A3mMSA {
                 if (pos < matches.length) {
                     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))) {
                             lcContent += c.toUpperCase();
                         }
                     }
-                    // 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));
@@ -235,9 +204,6 @@ export default class A3mMSA {
     getMSA() {
         return this.MSA;
     }
-    getRowData() {
-        return undefined;
-    }
     getNames() {
         return this.orderedNames;
     }
@@ -248,35 +214,5 @@ 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() {
-        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 [];
-    }
 }
 //# sourceMappingURL=A3mMSA.js.map

package/dist/msa/A3mMSA.js.map

@@ -1 +1 @@
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+{"version":3,"file":"A3mMSA.js","sourceRoot":"","sources":["../../src/msa/A3mMSA.ts"],"names":[],"mappings":"AAAA,OAAO,OAAO,MAAM,cAAc,CAAA;AAElC;;;;;;;;;;;;;;;;;;;;GAoBG;AAEH,MAAM,MAAM,GAAG,EAAE,CAAA,CAAC,MAAM;AACxB,MAAM,MAAM,GAAG,EAAE,CAAA,CAAC,MAAM;AACxB,MAAM,MAAM,GAAG,EAAE,CAAA,CAAC,MAAM;AACxB,MAAM,MAAM,GAAG,GAAG,CAAA,CAAC,MAAM;AACzB,MAAM,SAAS,GAAG,EAAE,CAAA,CAAC,MAAM;AAC3B,MAAM,QAAQ,GAAG,EAAE,CAAA,CAAC,MAAM;AAE1B,SAAS,OAAO,CAAC,IAAY;IAC3B,OAAO,IAAI,IAAI,MAAM,IAAI,IAAI,IAAI,MAAM,CAAA;AACzC,CAAC;AAED,MAAM,CAAC,OAAO,OAAO,MAAO,SAAQ,OAAO;IACjC,GAAG,CAAqC;IACxC,YAAY,CAAU;IAE9B,YAAY,IAAY;QACtB,KAAK,EAAE,CAAA;QACP,MAAM,OAAO,GAAa,EAAE,CAAA;QAC5B,MAAM,KAAK,GAAa,EAAE,CAAA;QAE1B,KAAK,MAAM,KAAK,IAAI,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,EAAE,CAAC;YACpC,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC;gBACtB,SAAQ;YACV,CAAC;YACD,MAAM,UAAU,GAAG,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,CAAA;YACtC,IAAI,UAAU,KAAK,CAAC,CAAC,EAAE,CAAC;gBACtB,SAAQ;YACV,CAAC;YACD,MAAM,OAAO,GAAG,KAAK,CAAC,KAAK,CAAC,CAAC,EAAE,UAAU,CAAC,CAAA;YAC1C,MAAM,QAAQ,GAAG,OAAO,CAAC,OAAO,CAAC,GAAG,CAAC,CAAA;YACrC,MAAM,EAAE,GAAG,QAAQ,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,EAAE,QAAQ,CAAC,CAAA;YACjE,IAAI,EAAE,EAAE,CAAC;gBACP,OAAO,CAAC,IAAI,CAAC,KAAK,CAAC,KAAK,CAAC,UAAU,GAAG,CAAC,CAAC,CAAC,UAAU,CAAC,KAAK,EAAE,EAAE,CAAC,CAAC,CAAA;gBAC/D,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;YAChB,CAAC;QACH,CAAC;QAED,IAAI,CAAC,YAAY,GAAG,KAAK,CAAA;QACzB,IAAI,CAAC,GAAG,GAAG,EAAE,OAAO,EAAE,IAAI,CAAC,SAAS,CAAC,OAAO,EAAE,KAAK,CAAC,EAAE,CAAA;IACxD,CAAC;IAED,MAAM,CAAC,KAAK,CAAC,IAAY;QACvB,IAAI,CAAC,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE,CAAC;YAC1B,OAAO,KAAK,CAAA;QACd,CAAC;QAED,MAAM,IAAI,GAAa,EAAE,CAAA;QACzB,KAAK,MAAM,KAAK,IAAI,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,EAAE,CAAC;YACpC,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC;gBACtB,SAAQ;YACV,CAAC;YACD,MAAM,UAAU,GAAG,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,CAAA;YACtC,IAAI,UAAU,KAAK,CAAC,CAAC,EAAE,CAAC;gBACtB,SAAQ;YACV,CAAC;YACD,MAAM,GAAG,GAAG,KAAK,CAAC,KAAK,CAAC,UAAU,GAAG,CAAC,CAAC,CAAC,UAAU,CAAC,KAAK,EAAE,EAAE,CAAC,CAAA;YAC7D,IAAI,GAAG,EAAE,CAAC;gBACR,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;YAChB,CAAC;QACH,CAAC;QAED,IAAI,IAAI,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;YACpB,OAAO,KAAK,CAAA;QACd,CAAC;QAED,IAAI,YAAY,GAAG,KAAK,CAAA;QACxB,IAAI,aAAa,GAAG,CAAC,CAAC,CAAA;QACtB,IAAI,eAAe,GAAG,IAAI,CAAA;QAE1B,KAAK,MAAM,GAAG,IAAI,IAAI,EAAE,CAAC;YACvB,IAAI,QAAQ,GAAG,CAAC,CAAA;YAChB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;gBACpC,MAAM,IAAI,GAAG,GAAG,CAAC,UAAU,CAAC,CAAC,CAAC,CAAA;gBAC9B,IAAI,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC;oBAClB,YAAY,GAAG,IAAI,CAAA;gBACrB,CAAC;qBAAM,IAAI,CAAC,IAAI,IAAI,MAAM,IAAI,IAAI,IAAI,MAAM,CAAC,IAAI,IAAI,KAAK,SAAS,EAAE,CAAC;oBACpE,QAAQ,EAAE,CAAA;gBACZ,CAAC;YACH,CAAC;YAED,IAAI,aAAa,KAAK,CAAC,CAAC,EAAE,CAAC;gBACzB,aAAa,GAAG,QAAQ,CAAA;YAC1B,CAAC;iBAAM,CAAC;gBACN,IAAI,QAAQ,KAAK,aAAa,EAAE,CAAC;oBAC/B,eAAe,GAAG,KAAK,CAAA;gBACzB,CAAC;YACH,CAAC;QACH,CAAC;QAED,OAAO,YAAY,IAAI,eAAe,CAAA;IACxC,CAAC;IAEO,SAAS,CACf,OAAiB,EACjB,KAAe;QAEf,MAAM,OAAO,GAAG,KAAK,CAAC,MAAM,CAAA;QAC5B,IAAI,OAAO,KAAK,CAAC,EAAE,CAAC;YAClB,OAAO,EAAE,CAAA;QACX,CAAC;QAED,MAAM,UAAU,GAAe,EAAE,CAAA;QACjC,MAAM,aAAa,GAAe,EAAE,CAAA;QAEpC,KAAK,IAAI,MAAM,GAAG,CAAC,EAAE,MAAM,GAAG,OAAO,EAAE,MAAM,EAAE,EAAE,CAAC;YAChD,MAAM,GAAG,GAAG,OAAO,CAAC,MAAM,CAAE,CAAA;YAC5B,MAAM,OAAO,GAAa,EAAE,CAAA;YAC5B,MAAM,OAAO,GAAa,EAAE,CAAA;YAC5B,IAAI,CAAC,GAAG,CAAC,CAAA;YAET,OAAO,CAAC,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC;gBACtB,MAAM,IAAI,GAAG,GAAG,CAAC,UAAU,CAAC,CAAC,CAAC,CAAA;gBAE9B,IAAI,CAAC,IAAI,IAAI,MAAM,IAAI,IAAI,IAAI,MAAM,CAAC,IAAI,IAAI,KAAK,SAAS,EAAE,CAAC;oBAC7D,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAE,CAAC,CAAA;oBACrB,IAAI,GAAG,GAAG,EAAE,CAAA;oBACZ,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,CAAA;oBACb,OAAO,CAAC,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC;wBACtB,MAAM,CAAC,GAAG,GAAG,CAAC,UAAU,CAAC,CAAC,CAAC,CAAA;wBAC3B,IAAI,OAAO,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,QAAQ,EAAE,CAAC;4BACjC,GAAG,IAAI,GAAG,CAAC,CAAC,CAAE,CAAA;4BACd,CAAC,EAAE,CAAA;wBACL,CAAC;6BAAM,CAAC;4BACN,MAAK;wBACP,CAAC;oBACH,CAAC;oBACD,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;oBACjB,CAAC,GAAG,CAAC,CAAA;gBACP,CAAC;qBAAM,IAAI,IAAI,KAAK,QAAQ,EAAE,CAAC;oBAC7B,CAAC,EAAE,CAAA;gBACL,CAAC;qBAAM,IAAI,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC;oBACzB,IAAI,GAAG,GAAG,EAAE,CAAA;oBACZ,OAAO,CAAC,GAAG,GAAG,CAAC,MAAM,IAAI,OAAO,CAAC,GAAG,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC;wBACpD,GAAG,IAAI,GAAG,CAAC,CAAC,CAAE,CAAA;wBACd,CAAC,EAAE,CAAA;oBACL,CAAC;oBACD,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;oBAChB,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;gBACnB,CAAC;qBAAM,CAAC;oBACN,CAAC,EAAE,CAAA;gBACL,CAAC;YACH,CAAC;YAED,UAAU,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;YACxB,aAAa,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;QAC7B,CAAC;QAED,MAAM,YAAY,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,UAAU,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,MAAM,CAAC,EAAE,CAAC,CAAC,CAAA;QAElE,MAAM,UAAU,GAAG,IAAI,KAAK,CAAS,YAAY,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;QAC1D,KAAK,IAAI,MAAM,GAAG,CAAC,EAAE,MAAM,GAAG,OAAO,EAAE,MAAM,EAAE,EAAE,CAAC;YAChD,MAAM,OAAO,GAAG,aAAa,CAAC,MAAM,CAAE,CAAA;YACtC,KAAK,IAAI,GAAG,GAAG,CAAC,EAAE,GAAG,GAAG,OAAO,CAAC,MAAM,EAAE,GAAG,EAAE,EAAE,CAAC;gBAC9C,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package/dist/msa/BaseMSA.d.ts

@@ -0,0 +1,19 @@
+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;
+    getRowData(_name: string): {
+        name?: string;
+        accession?: string;
+        dbxref?: string;
+    } | undefined;
+    getStructures(): Record<string, unknown>;
+    getHeader(): unknown;
+    get alignmentNames(): string[];
+    get seqConsensus(): string | undefined;
+    get secondaryStructureConsensus(): string | undefined;
+    get tracks(): unknown[];
+}

package/dist/{src/msa/EmfMSA.js → msa/BaseMSA.js}

@@ -1,33 +1,4 @@
-import { parseEmfAln } from 'emf-js';
-export default class EmfMSA {
-    MSA;
-    constructor(text) {
-        this.MSA = parseEmfAln(text);
-    }
-    getMSA() {
-        return this.MSA;
-    }
-    getRow(name) {
-        return this.MSA.find(aln => aln.protein === name)?.seq || '';
-    }
-    getWidth() {
-        return this.MSA[0].seq.length;
-    }
-    getRowData() {
-        return undefined;
-    }
-    getHeader() {
-        return '';
-    }
-    getNames() {
-        return this.MSA.map(aln => aln.protein);
-    }
-    getStructures() {
-        return {};
-    }
-    get alignmentNames() {
-        return [];
-    }
+export default class BaseMSA {
     getTree() {
         return {
             id: 'root',
@@ -35,11 +6,23 @@ export default class EmfMSA {
             noTree: true,
             children: this.getNames().map(name => ({
                 id: name,
-                name,
                 children: [],
+                name,
             })),
         };
     }
+    getRowData(_name) {
+        return undefined;
+    }
+    getStructures() {
+        return {};
+    }
+    getHeader() {
+        return {};
+    }
+    get alignmentNames() {
+        return [];
+    }
     get seqConsensus() {
         return undefined;
     }
@@ -50,4 +33,4 @@ export default class EmfMSA {
         return [];
     }
 }
-//# sourceMappingURL=EmfMSA.js.map
+//# sourceMappingURL=BaseMSA.js.map

package/dist/msa/BaseMSA.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"BaseMSA.js","sourceRoot":"","sources":["../../src/msa/BaseMSA.ts"],"names":[],"mappings":"AAEA,MAAM,CAAC,OAAO,OAAgB,OAAO;IAMnC,OAAO;QACL,OAAO;YACL,EAAE,EAAE,MAAM;YACV,IAAI,EAAE,MAAM;YACZ,MAAM,EAAE,IAAI;YACZ,QAAQ,EAAE,IAAI,CAAC,QAAQ,EAAE,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;gBACrC,EAAE,EAAE,IAAI;gBACR,QAAQ,EAAE,EAAE;gBACZ,IAAI;aACL,CAAC,CAAC;SACJ,CAAA;IACH,CAAC;IAED,UAAU,CAAC,KAAa;QACtB,OAAO,SAA+E,CAAA;IACxF,CAAC;IAED,aAAa;QACX,OAAO,EAAE,CAAA;IACX,CAAC;IAED,SAAS;QACP,OAAO,EAAE,CAAA;IACX,CAAC;IAED,IAAI,cAAc;QAChB,OAAO,EAAE,CAAA;IACX,CAAC;IAED,IAAI,YAAY;QACd,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,IAAI,2BAA2B;QAC7B,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,IAAI,MAAM;QACR,OAAO,EAAE,CAAA;IACX,CAAC;CACF"}

package/dist/msa/ClustalMSA.d.ts

@@ -1,5 +1,5 @@
-import type { NodeWithIds } from '../types.ts';
-export default class ClustalMSA {
+import BaseMSA from './BaseMSA.ts';
+export default class ClustalMSA extends BaseMSA {
     private MSA;
     constructor(text: string);
     getMSA(): {
@@ -15,16 +15,10 @@ export default class ClustalMSA {
     };
     getRow(name: string): string;
     getWidth(): number;
-    getRowData(): undefined;
     getHeader(): {
         info: string;
         version: string | undefined;
     };
     getNames(): string[];
-    getStructures(): {};
-    get alignmentNames(): never[];
-    getTree(): NodeWithIds;
     get seqConsensus(): string;
-    get secondaryStructureConsensus(): undefined;
-    get tracks(): never[];
 }

package/dist/msa/ClustalMSA.js

@@ -1,7 +1,9 @@
 import { parse } from 'clustal-js';
-export default class ClustalMSA {
+import BaseMSA from "./BaseMSA.js";
+export default class ClustalMSA extends BaseMSA {
     MSA;
     constructor(text) {
+        super();
         this.MSA = parse(text);
     }
     getMSA() {
@@ -13,41 +15,14 @@ export default class ClustalMSA {
     getWidth() {
         return this.MSA.alns[0].seq.length;
     }
-    getRowData() {
-        return undefined;
-    }
     getHeader() {
         return this.MSA.header;
     }
     getNames() {
         return this.MSA.alns.map(aln => aln.id);
     }
-    getStructures() {
-        return {};
-    }
-    get alignmentNames() {
-        return [];
-    }
-    getTree() {
-        return {
-            id: 'root',
-            name: 'root',
-            noTree: true,
-            children: this.getNames().map(name => ({
-                id: name,
-                name,
-                children: [],
-            })),
-        };
-    }
     get seqConsensus() {
         return this.MSA.consensus;
     }
-    get secondaryStructureConsensus() {
-        return undefined;
-    }
-    get tracks() {
-        return [];
-    }
 }
 //# sourceMappingURL=ClustalMSA.js.map

package/dist/msa/ClustalMSA.js.map

@@ -1 +1 @@
-{"version":3,"file":"ClustalMSA.js","sourceRoot":"","sources":["../../src/msa/ClustalMSA.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,YAAY,CAAA;AAIlC,MAAM,CAAC,OAAO,OAAO,UAAU;IACrB,GAAG,CAA0B;IAErC,YAAY,IAAY;QACtB,IAAI,CAAC,GAAG,GAAG,KAAK,CAAC,IAAI,CAAC,CAAA;IACxB,CAAC;IAED,MAAM;QACJ,OAAO,IAAI,CAAC,GAAG,CAAA;IACjB,CAAC;IAED,MAAM,CAAC,IAAY;QACjB,OAAO,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,KAAK,IAAI,CAAC,EAAE,GAAG,IAAI,EAAE,CAAA;IAC9D,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,CAAE,CAAC,GAAG,CAAC,MAAM,CAAA;IACrC,CAAC;IAED,UAAU;QACR,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,SAAS;QACP,OAAO,IAAI,CAAC,GAAG,CAAC,MAAM,CAAA;IACxB,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,CAAA;IACzC,CAAC;IAED,aAAa;QACX,OAAO,EAAE,CAAA;IACX,CAAC;IAED,IAAI,cAAc;QAChB,OAAO,EAAE,CAAA;IACX,CAAC;IAED,OAAO;QACL,OAAO;YACL,EAAE,EAAE,MAAM;YACV,IAAI,EAAE,MAAM;YACZ,MAAM,EAAE,IAAI;YACZ,QAAQ,EAAE,IAAI,CAAC,QAAQ,EAAE,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;gBACrC,EAAE,EAAE,IAAI;gBACR,IAAI;gBACJ,QAAQ,EAAE,EAAE;aACb,CAAC,CAAC;SACJ,CAAA;IACH,CAAC;IAED,IAAI,YAAY;QACd,OAAO,IAAI,CAAC,GAAG,CAAC,SAAS,CAAA;IAC3B,CAAC;IACD,IAAI,2BAA2B;QAC7B,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,IAAI,MAAM;QACR,OAAO,EAAE,CAAA;IACX,CAAC;CACF"}
+{"version":3,"file":"ClustalMSA.js","sourceRoot":"","sources":["../../src/msa/ClustalMSA.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,YAAY,CAAA;AAElC,OAAO,OAAO,MAAM,cAAc,CAAA;AAElC,MAAM,CAAC,OAAO,OAAO,UAAW,SAAQ,OAAO;IACrC,GAAG,CAA0B;IAErC,YAAY,IAAY;QACtB,KAAK,EAAE,CAAA;QACP,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,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,IAAI,YAAY;QACd,OAAO,IAAI,CAAC,GAAG,CAAC,SAAS,CAAA;IAC3B,CAAC;CACF"}

package/dist/msa/EmfMSA.d.ts

@@ -1,5 +1,5 @@
-import type { NodeWithIds } from '../types.ts';
-export default class EmfMSA {
+import BaseMSA from './BaseMSA.ts';
+export default class EmfMSA extends BaseMSA {
     private MSA;
     constructor(text: string);
     getMSA(): {
@@ -15,13 +15,6 @@ export default class EmfMSA {
     }[];
     getRow(name: string): string;
     getWidth(): number;
-    getRowData(): undefined;
     getHeader(): string;
     getNames(): string[];
-    getStructures(): {};
-    get alignmentNames(): never[];
-    getTree(): NodeWithIds;
-    get seqConsensus(): undefined;
-    get secondaryStructureConsensus(): undefined;
-    get tracks(): never[];
 }

package/dist/msa/EmfMSA.js

@@ -1,7 +1,9 @@
 import { parseEmfAln } from 'emf-js';
-export default class EmfMSA {
+import BaseMSA from "./BaseMSA.js";
+export default class EmfMSA extends BaseMSA {
     MSA;
     constructor(text) {
+        super();
         this.MSA = parseEmfAln(text);
     }
     getMSA() {
@@ -13,41 +15,11 @@ export default class EmfMSA {
     getWidth() {
         return this.MSA[0].seq.length;
     }
-    getRowData() {
-        return undefined;
-    }
     getHeader() {
         return '';
     }
     getNames() {
         return this.MSA.map(aln => aln.protein);
     }
-    getStructures() {
-        return {};
-    }
-    get alignmentNames() {
-        return [];
-    }
-    getTree() {
-        return {
-            id: 'root',
-            name: 'root',
-            noTree: true,
-            children: this.getNames().map(name => ({
-                id: name,
-                name,
-                children: [],
-            })),
-        };
-    }
-    get seqConsensus() {
-        return undefined;
-    }
-    get secondaryStructureConsensus() {
-        return undefined;
-    }
-    get tracks() {
-        return [];
-    }
 }
 //# sourceMappingURL=EmfMSA.js.map

package/dist/msa/EmfMSA.js.map

@@ -1 +1 @@
-{"version":3,"file":"EmfMSA.js","sourceRoot":"","sources":["../../src/msa/EmfMSA.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAE,MAAM,QAAQ,CAAA;AAIpC,MAAM,CAAC,OAAO,OAAO,MAAM;IACjB,GAAG,CAAgC;IAE3C,YAAY,IAAY;QACtB,IAAI,CAAC,GAAG,GAAG,WAAW,CAAC,IAAI,CAAC,CAAA;IAC9B,CAAC;IAED,MAAM;QACJ,OAAO,IAAI,CAAC,GAAG,CAAA;IACjB,CAAC;IAED,MAAM,CAAC,IAAY;QACjB,OAAO,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,OAAO,KAAK,IAAI,CAAC,EAAE,GAAG,IAAI,EAAE,CAAA;IAC9D,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,GAAG,CAAC,CAAC,CAAE,CAAC,GAAG,CAAC,MAAM,CAAA;IAChC,CAAC;IAED,UAAU;QACR,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,SAAS;QACP,OAAO,EAAE,CAAA;IACX,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;IACzC,CAAC;IAED,aAAa;QACX,OAAO,EAAE,CAAA;IACX,CAAC;IAED,IAAI,cAAc;QAChB,OAAO,EAAE,CAAA;IACX,CAAC;IAED,OAAO;QACL,OAAO;YACL,EAAE,EAAE,MAAM;YACV,IAAI,EAAE,MAAM;YACZ,MAAM,EAAE,IAAI;YACZ,QAAQ,EAAE,IAAI,CAAC,QAAQ,EAAE,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;gBACrC,EAAE,EAAE,IAAI;gBACR,IAAI;gBACJ,QAAQ,EAAE,EAAE;aACb,CAAC,CAAC;SACJ,CAAA;IACH,CAAC;IAED,IAAI,YAAY;QACd,OAAO,SAAS,CAAA;IAClB,CAAC;IACD,IAAI,2BAA2B;QAC7B,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,IAAI,MAAM;QACR,OAAO,EAAE,CAAA;IACX,CAAC;CACF"}
+{"version":3,"file":"EmfMSA.js","sourceRoot":"","sources":["../../src/msa/EmfMSA.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAE,MAAM,QAAQ,CAAA;AAEpC,OAAO,OAAO,MAAM,cAAc,CAAA;AAElC,MAAM,CAAC,OAAO,OAAO,MAAO,SAAQ,OAAO;IACjC,GAAG,CAAgC;IAE3C,YAAY,IAAY;QACtB,KAAK,EAAE,CAAA;QACP,IAAI,CAAC,GAAG,GAAG,WAAW,CAAC,IAAI,CAAC,CAAA;IAC9B,CAAC;IAED,MAAM;QACJ,OAAO,IAAI,CAAC,GAAG,CAAA;IACjB,CAAC;IAED,MAAM,CAAC,IAAY;QACjB,OAAO,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,OAAO,KAAK,IAAI,CAAC,EAAE,GAAG,IAAI,EAAE,CAAA;IAC9D,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,GAAG,CAAC,CAAC,CAAE,CAAC,GAAG,CAAC,MAAM,CAAA;IAChC,CAAC;IAED,SAAS;QACP,OAAO,EAAE,CAAA;IACX,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;IACzC,CAAC;CACF"}

package/dist/msa/FastaMSA.d.ts

@@ -1,20 +1,12 @@
-import type { NodeWithIds } from '../types.ts';
-export default class FastaMSA {
+import BaseMSA from './BaseMSA.ts';
+export default class FastaMSA extends BaseMSA {
     private MSA;
     constructor(text: string);
     getMSA(): {
         seqdata: Record<string, string>;
         colonNormalized: Record<string, string>;
     };
-    getRowData(): undefined;
     getNames(): string[];
     getRow(name: string): string;
     getWidth(): number;
-    getStructures(): {};
-    get alignmentNames(): never[];
-    getHeader(): {};
-    getTree(): NodeWithIds;
-    get seqConsensus(): undefined;
-    get secondaryStructureConsensus(): undefined;
-    get tracks(): never[];
 }

package/dist/msa/FastaMSA.js

@@ -1,6 +1,8 @@
-export default class FastaMSA {
+import BaseMSA from "./BaseMSA.js";
+export default class FastaMSA extends BaseMSA {
     MSA;
     constructor(text) {
+        super();
         const seqdata = {};
         const colonNormalized = {};
         for (const entry of text.split('>')) {
@@ -26,9 +28,6 @@ export default class FastaMSA {
     getMSA() {
         return this.MSA;
     }
-    getRowData() {
-        return undefined;
-    }
     getNames() {
         return Object.keys(this.MSA.seqdata);
     }
@@ -41,35 +40,5 @@ 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() {
-        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 [];
-    }
 }
 //# sourceMappingURL=FastaMSA.js.map

package/dist/msa/FastaMSA.js.map

@@ -1 +1 @@
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