clustal-js - npm Package Compare versions

Comparing version 2.0.1 to 2.0.2

dist/index.d.ts

 export declare function parseClustalIter(arr: Iterator<string>): {
     consensus: string;
     alns: {
-        id: any;
-        seq: any;
+        id: string;
+        seq: string;
     }[];
@@ -12,8 +12,9 @@ header: {
 };
+interface Row {
+    id: string;
+    seq: string;
+}
 export declare function parsePairwiseIter(arr: string): {
     consensus: string;
-    alns: {
-        id: any;
-        seq: any;
-    }[];
+    alns: [Row, Row];
 };
@@ -23,4 +24,4 @@ export declare function parse(contents: string): {
     alns: {
-        id: any;
-        seq: any;
+        id: string;
+        seq: string;
     }[];
@@ -34,6 +35,4 @@ header: {
     consensus: string;
-    alns: {
-        id: any;
-        seq: any;
-    }[];
+    alns: [Row, Row];
 };
+export {};

dist/index.js

 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.parsePairwise = exports.parse = exports.parsePairwiseIter = exports.parseClustalIter = void 0;
+exports.parseClustalIter = parseClustalIter;
+exports.parsePairwiseIter = parsePairwiseIter;
+exports.parse = parse;
+exports.parsePairwise = parsePairwise;
 const pairwise_1 = require("./pairwise");
@@ -23,3 +26,2 @@ const util_1 = require("./util");
 }
-exports.parseClustalIter = parseClustalIter;
 function parsePairwiseIter(arr) {
@@ -35,5 +37,10 @@ const res = (0, pairwise_1.parsePairwiseBlocks)(arr.split('\n')[Symbol.iterator]());
     }
-    return { consensus, alns };
+    if (alns.length !== 2) {
+        throw new Error('More than two sequences in pairwise alignment');
+    }
+    return {
+        consensus,
+        alns: alns,
+    };
 }
-exports.parsePairwiseIter = parsePairwiseIter;
 function parse(contents) {
@@ -43,10 +50,8 @@ const iter = contents.split('\n')[Symbol.iterator]();
 }
-exports.parse = parse;
 function parsePairwise(contents) {
-    const res = contents
+    return parsePairwiseIter(contents
         .split('\n')
         .filter(f => !f.startsWith('#'))
-        .join('\n');
-    return parsePairwiseIter(res);
+        .join('\n'));
 }
-exports.parsePairwise = parsePairwise;
+//# sourceMappingURL=index.js.map

dist/pairwise.d.ts

 export declare function getSeqBounds(line: string): readonly [number, number];
 export declare function parsePairwiseBlock(arr: Iterator<string>): {
-    ids: any[];
-    seqs: any[];
+    ids: string[];
+    seqs: string[];
     consensus: string;
 } | undefined;
 export declare function parsePairwiseBlocks(arr: Iterator<string>): {
-    ids: any[];
-    seqs: any[];
+    ids: string[];
+    seqs: string[];
     consensus: string;
 } | undefined;

dist/pairwise.js

 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.parsePairwiseBlocks = exports.parsePairwiseBlock = exports.getSeqBounds = void 0;
+exports.getSeqBounds = getSeqBounds;
+exports.parsePairwiseBlock = parsePairwiseBlock;
+exports.parsePairwiseBlocks = parsePairwiseBlocks;
 const util_1 = require("./util");
@@ -13,3 +15,2 @@ function getSeqBounds(line) {
 }
-exports.getSeqBounds = getSeqBounds;
 // Use the first block to get the sequence identifiers
@@ -24,7 +25,7 @@ function parsePairwiseBlock(arr) {
     while (line) {
-        if (line[0] !== ' ') {
-            block.push(line);
+        if (line.startsWith(' ')) {
+            consensusLine = line;
         }
         else {
-            consensusLine = line;
+            block.push(line);
         }
@@ -45,3 +46,2 @@ line = arr.next().value;
 }
-exports.parsePairwiseBlock = parsePairwiseBlock;
 function parsePairwiseBlocks(arr) {
@@ -60,2 +60,2 @@ let block;
 }
-exports.parsePairwiseBlocks = parsePairwiseBlocks;
+//# sourceMappingURL=pairwise.js.map

dist/util.d.ts

@@ -6,13 +6,13 @@ export declare function parseVersion(line: string): string;
 };
-export declare function getFirstNonEmptyLine(arr: Iterator<string>): any;
+export declare function getFirstNonEmptyLine(arr: Iterator<string>): string;
 export declare function getSeqBounds(line: string): readonly [number, number];
 export declare function parseBlock(arr: Iterator<string>): {
-    ids: any[];
-    seqs: any[];
+    ids: string[];
+    seqs: string[];
     consensus: string;
 } | undefined;
 export declare function parseBlocks(arr: Iterator<string>): {
-    ids: any[];
-    seqs: any[];
+    ids: string[];
+    seqs: string[];
     consensus: string;
 } | undefined;

dist/util.js

 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.parseBlocks = exports.parseBlock = exports.getSeqBounds = exports.getFirstNonEmptyLine = exports.parseHeader = exports.parseVersion = void 0;
+exports.parseVersion = parseVersion;
+exports.parseHeader = parseHeader;
+exports.getFirstNonEmptyLine = getFirstNonEmptyLine;
+exports.getSeqBounds = getSeqBounds;
+exports.parseBlock = parseBlock;
+exports.parseBlocks = parseBlocks;
 function parseVersion(line) {
-    const res = line.match(/\(?(\d+(\.\d+)+)\)?/);
+    const res = /\(?(\d+(\.\d+)+)\)?/.exec(line);
     return res && res.length > 1 ? res[1] : '';
 }
-exports.parseVersion = parseVersion;
 function parseHeader(info) {
@@ -17,3 +21,2 @@ const knownHeaders = ['CLUSTAL', 'PROBCONS', 'MUSCLE', 'MSAPROBS', 'Kalign'];
 }
-exports.parseHeader = parseHeader;
 function getFirstNonEmptyLine(arr) {
@@ -27,3 +30,2 @@ // There should be two blank lines after the header line
 }
-exports.getFirstNonEmptyLine = getFirstNonEmptyLine;
 function getSeqBounds(line) {
@@ -36,3 +38,2 @@ const fields = line.split(/\s+/);
 }
-exports.getSeqBounds = getSeqBounds;
 // Use the first block to get the sequence identifiers
@@ -47,7 +48,7 @@ function parseBlock(arr) {
     while (line) {
-        if (line[0] !== ' ') {
-            block.push(line);
+        if (line[0].startsWith(' ')) {
+            consensusLine = line;
         }
         else {
-            consensusLine = line;
+            block.push(line);
         }
@@ -68,3 +69,2 @@ line = arr.next().value;
 }
-exports.parseBlock = parseBlock;
 function parseBlocks(arr) {
@@ -83,2 +83,2 @@ let block;
 }
-exports.parseBlocks = parseBlocks;
+//# sourceMappingURL=util.js.map

package.json

 {
   "name": "clustal-js",
-  "version": "2.0.1",
+  "version": "2.0.2",
   "main": "dist/index.js",
+  "module": "esm/index.js",
   "repository": "cmdcolin/clustal-js",
   "files": [
-    "dist"
+    "dist",
+    "esm",
+    "src"
   ],
@@ -12,19 +15,21 @@ "license": "MIT",
     "@types/jest": "^29.5.12",
-    "@types/node": "^20.11.16",
-    "@typescript-eslint/eslint-plugin": "^6.21.0",
-    "@typescript-eslint/parser": "^6.21.0",
-    "eslint": "^8.56.0",
-    "eslint-config-prettier": "^9.1.0",
-    "eslint-plugin-prettier": "^5.1.3",
-    "eslint-plugin-unicorn": "^50.0.1",
+    "@types/node": "^22.0.0",
+    "@typescript-eslint/eslint-plugin": "^8.1.0",
+    "@typescript-eslint/parser": "^8.1.0",
+    "eslint": "^9.9.0",
+    "eslint-plugin-unicorn": "^55.0.0",
     "jest": "^29.7.0",
     "prettier": "^3.2.5",
-    "ts-jest": "^29.1.2",
-    "typescript": "^5.3.3"
+    "rimraf": "^6.0.1",
+    "ts-jest": "^29.2.4",
+    "typescript": "^5.3.3",
+    "typescript-eslint": "^8.1.0"
   },
   "scripts": {
-    "clean": "rimraf dist",
+    "clean": "rimraf dist esm",
     "test": "jest",
-    "lint": "eslint --ext .ts src test",
-    "build": "tsc",
+    "lint": "eslint --report-unused-disable-directives --max-warnings 0",
+    "build": "npm run build:esm && npm run build:es5",
+    "build:esm": "tsc --target es2018 --outDir esm",
+    "build:es5": "tsc --target es2015 --module commonjs --outDir dist",
     "prebuild": "npm run clean",
@@ -31,0 +36,0 @@ "preversion": "npm run lint && npm test && npm run build",

README.md

@@ -1,2 +0,3 @@
-[![Build Status](https://travis-ci.com/cmdcolin/clustal-js.svg?branch=master)](https://travis-ci.com/cmdcolin/clustal-js)
+[![NPM version](https://img.shields.io/npm/v/@gmod/bam.svg?style=flat-square)](https://npmjs.org/package/@gmod/bam)
+[![Build Status](https://img.shields.io/github/actions/workflow/status/cmdcolin/clustal-js/push.yml?branch=master)](https://github.com/cmdcolin/clustal-js/actions?query=branch%3Amaster+workflow%3APush+)
 
@@ -3,0 +4,0 @@ # clustal-js

New alerts

License Policy Violation

License

This package is not allowed per your license policy. Review the package's license to ensure compliance.

Found 1 instance in 1 package

Major refactor

Supply chain risk

Package has recently undergone a major refactor. It may be unstable or indicate significant internal changes. Use caution when updating to versions that include significant changes.

Found 1 instance in 1 package

Fixed alerts

License Policy Violation

License

This package is not allowed per your license policy. Review the package's license to ensure compliance.

Found 1 instance in 1 package

Major refactor

Supply chain risk

Package has recently undergone a major refactor. It may be unstable or indicate significant internal changes. Use caution when updating to versions that include significant changes.

Found 1 instance in 1 package

Improved metrics

Total package byte prevSize

42806

increased by185.47%

Number of package files

24

increased by166.67%

Lines of code

658

increased by165.32%

Number of lines in readme file

161

increased by0.63%

No dependency changes