clustal-js - npm Package Compare versions

Comparing version 1.0.2 to 1.0.3

CHANGELOG.md

@@ -0,1 +1,6 @@
+# v1.0.3
+
+- Add generated typescript declarations to output
+
+
 ## v1.0.2
@@ -2,0 +7,0 @@

dist/index.js

@@ -1,29 +0,25 @@
-import { parseBlocks, parseHeader, getFirstNonEmptyLine } from "./util";
-export function parseIter(arr) {
-  const line = getFirstNonEmptyLine(arr);
-  if (!line) throw new Error("Empty file received");
-  const header = parseHeader(line);
-  const res = parseBlocks(arr);
-  if (res === undefined) throw new Error("No blocks parsed");
-  const alns = res.seqs.map((n, index) => ({
-    id: res.ids[index],
-    seq: n
-  }));
-  const {
-    consensus
-  } = res;
-
-  if (consensus.length != alns[0].seq.length) {
-    throw new Error(`Consensus length != sequence length. Con ${consensus.length} seq ${alns[0].seq.length}`);
-  }
-
-  return {
-    consensus,
-    alns,
-    header
-  };
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.parse = exports.parseIter = void 0;
+const util_1 = require("./util");
+function parseIter(arr) {
+    const line = util_1.getFirstNonEmptyLine(arr);
+    if (!line)
+        throw new Error("Empty file received");
+    const header = util_1.parseHeader(line);
+    const res = util_1.parseBlocks(arr);
+    if (res === undefined)
+        throw new Error("No blocks parsed");
+    const alns = res.seqs.map((n, index) => ({ id: res.ids[index], seq: n }));
+    const { consensus } = res;
+    if (consensus.length != alns[0].seq.length) {
+        throw new Error(`Consensus length != sequence length. Con ${consensus.length} seq ${alns[0].seq.length}`);
+    }
+    return { consensus, alns, header };
 }
-export function parse(contents) {
-  const iter = contents.split("\n")[Symbol.iterator]();
-  return parseIter(iter);
-}
+exports.parseIter = parseIter;
+function parse(contents) {
+    const iter = contents.split("\n")[Symbol.iterator]();
+    return parseIter(iter);
+}
+exports.parse = parse;

dist/util.js

@@ -1,80 +0,75 @@
-export function parseVersion(line) {
-  const res = line.match(/\(?(\d+(\.\d+)+)\)?/);
-  return res && res.length > 1 ? res[1] : "";
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.parseBlocks = exports.parseBlock = exports.getSeqBounds = exports.getFirstNonEmptyLine = exports.parseHeader = exports.parseVersion = void 0;
+function parseVersion(line) {
+    const res = line.match(/\(?(\d+(\.\d+)+)\)?/);
+    return res && res.length > 1 ? res[1] : "";
 }
-export function parseHeader(info) {
-  const knownHeaders = ["CLUSTAL", "PROBCONS", "MUSCLE", "MSAPROBS", "Kalign"];
-
-  if (!knownHeaders.find(l => info.startsWith(l))) {
-    console.warn(`${info} is not a known CLUSTAL header: ${knownHeaders.join(",")}, proceeding but could indicate an issue`);
-  }
-
-  const version = parseVersion(info);
-  return {
-    info,
-    version
-  };
+exports.parseVersion = parseVersion;
+function parseHeader(info) {
+    const knownHeaders = ["CLUSTAL", "PROBCONS", "MUSCLE", "MSAPROBS", "Kalign"];
+    if (!knownHeaders.find((l) => info.startsWith(l))) {
+        console.warn(`${info} is not a known CLUSTAL header: ${knownHeaders.join(",")}, proceeding but could indicate an issue`);
+    }
+    const version = parseVersion(info);
+    return { info, version };
 }
-export function getFirstNonEmptyLine(arr) {
-  // There should be two blank lines after the header line
-  let line = arr.next();
-
-  while (!line.done && line.value.trim() === "") {
-    line = arr.next();
-  }
-
-  return line.value;
+exports.parseHeader = parseHeader;
+function getFirstNonEmptyLine(arr) {
+    // There should be two blank lines after the header line
+    let line = arr.next();
+    while (!line.done && line.value.trim() === "") {
+        line = arr.next();
+    }
+    return line.value;
 }
-export function getSeqBounds(line) {
-  const fields = line.split(/\s+/);
-  const temp = line.slice(fields[0].length);
-  const s = fields[0].length + temp.indexOf(fields[1]);
-  const e = s + fields[1].length;
-  return [s, e];
-} // Use the first block to get the sequence identifiers
-
-export function parseBlock(arr) {
-  let line = getFirstNonEmptyLine(arr);
-  const block = [];
-  let consensusLine = "";
-  if (!line) return undefined;
-
-  while (line) {
-    if (line[0] !== " ") block.push(line);else consensusLine = line;
-    line = arr.next().value;
-  }
-
-  const [start, end] = getSeqBounds(block[0]);
-  const fields = block.map(s => s.split(/\s+/));
-  const ids = fields.map(s => s[0]);
-  const seqs = block.map(s => s.slice(start, end));
-  let consensus = consensusLine.slice(start, end); // handle if the consensus trailing whitespace got trimmed
-
-  const remainder = seqs[0].length - consensus.length;
-
-  if (remainder) {
-    consensus += " ".repeat(remainder);
-  }
-
-  return {
-    ids,
-    seqs,
-    consensus
-  };
+exports.getFirstNonEmptyLine = getFirstNonEmptyLine;
+function getSeqBounds(line) {
+    const fields = line.split(/\s+/);
+    const temp = line.slice(fields[0].length);
+    const s = fields[0].length + temp.indexOf(fields[1]);
+    const e = s + fields[1].length;
+    return [s, e];
 }
-export function parseBlocks(arr) {
-  let block;
-  const res = parseBlock(arr);
-
-  if (res !== undefined) {
-    while (block = parseBlock(arr)) {
-      for (let i = 0; i < block.seqs.length; i++) {
-        res.seqs[i] += block.seqs[i];
-      }
-
-      res.consensus += block.consensus;
+exports.getSeqBounds = getSeqBounds;
+// Use the first block to get the sequence identifiers
+function parseBlock(arr) {
+    let line = getFirstNonEmptyLine(arr);
+    const block = [];
+    let consensusLine = "";
+    if (!line)
+        return undefined;
+    while (line) {
+        if (line[0] !== " ")
+            block.push(line);
+        else
+            consensusLine = line;
+        line = arr.next().value;
     }
-  }
-
-  return res;
-}
+    const [start, end] = getSeqBounds(block[0]);
+    const fields = block.map((s) => s.split(/\s+/));
+    const ids = fields.map((s) => s[0]);
+    const seqs = block.map((s) => s.slice(start, end));
+    let consensus = consensusLine.slice(start, end);
+    // handle if the consensus trailing whitespace got trimmed
+    const remainder = seqs[0].length - consensus.length;
+    if (remainder) {
+        consensus += " ".repeat(remainder);
+    }
+    return { ids, seqs, consensus };
+}
+exports.parseBlock = parseBlock;
+function parseBlocks(arr) {
+    let block;
+    const res = parseBlock(arr);
+    if (res !== undefined) {
+        while ((block = parseBlock(arr))) {
+            for (let i = 0; i < block.seqs.length; i++) {
+                res.seqs[i] += block.seqs[i];
+            }
+            res.consensus += block.consensus;
+        }
+    }
+    return res;
+}
+exports.parseBlocks = parseBlocks;

package.json

 {
   "name": "clustal-js",
-  "version": "1.0.2",
+  "version": "1.0.3",
   "main": "dist/index.js",
+  "repository": "cmdcolin/clustal-js",
   "files": [
@@ -6,0 +7,0 @@ "dist"

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Improved metrics

Total package byte prevSize

8256

increased by28.42%

Number of package files

9

increased by50%

Lines of code

130

increased by41.3%

Number of medium supply chain risk alerts

0

decreased by-100%

No dependency changes