clustal-js 2.0.6 → 2.0.7

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Files changed (18) hide show
  1. package/dist/index.js +16 -16
  2. package/dist/index.js.map +1 -1
  3. package/dist/package.json +1 -0
  4. package/dist/pairwise.d.ts +1 -1
  5. package/dist/pairwise.js +35 -25
  6. package/dist/pairwise.js.map +1 -1
  7. package/dist/util.js +24 -24
  8. package/dist/util.js.map +1 -1
  9. package/esm/index.js +26 -20
  10. package/esm/index.js.map +1 -1
  11. package/esm/pairwise.d.ts +1 -1
  12. package/esm/pairwise.js +42 -27
  13. package/esm/pairwise.js.map +1 -1
  14. package/esm/util.js +38 -30
  15. package/esm/util.js.map +1 -1
  16. package/package.json +22 -13
  17. package/src/index.ts +2 -2
  18. package/src/pairwise.ts +31 -17
package/dist/index.js CHANGED
@@ -4,51 +4,51 @@ exports.parseClustalIter = parseClustalIter;
4
4
  exports.parsePairwiseIter = parsePairwiseIter;
5
5
  exports.parse = parse;
6
6
  exports.parsePairwise = parsePairwise;
7
- const pairwise_1 = require("./pairwise");
8
- const util_1 = require("./util");
7
+ var pairwise_ts_1 = require("./pairwise.js");
8
+ var util_ts_1 = require("./util.js");
9
9
  function parseClustalIter(arr) {
10
- const line = (0, util_1.getFirstNonEmptyLine)(arr);
10
+ var line = (0, util_ts_1.getFirstNonEmptyLine)(arr);
11
11
  if (!line) {
12
12
  throw new Error('Empty file received');
13
13
  }
14
- const header = (0, util_1.parseHeader)(line);
15
- const res = (0, util_1.parseBlocks)(arr);
14
+ var header = (0, util_ts_1.parseHeader)(line);
15
+ var res = (0, util_ts_1.parseBlocks)(arr);
16
16
  if (res === undefined) {
17
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  throw new Error('No blocks parsed');
18
18
  }
19
- const alns = res.seqs.map((n, index) => ({ id: res.ids[index], seq: n }));
20
- const { consensus } = res;
19
+ var alns = res.seqs.map(function (n, index) { return ({ id: res.ids[index], seq: n }); });
20
+ var consensus = res.consensus;
21
21
  if (consensus.length != alns[0].seq.length) {
22
- throw new Error(`Consensus length != sequence length. Con ${consensus.length} seq ${alns[0].seq.length}`);
22
+ throw new Error("Consensus length != sequence length. Con ".concat(consensus.length, " seq ").concat(alns[0].seq.length));
23
23
  }
24
- return { consensus, alns, header };
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+ return { consensus: consensus, alns: alns, header: header };
25
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  }
26
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  function parsePairwiseIter(arr) {
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- const res = (0, pairwise_1.parsePairwiseBlocks)(arr.split('\n')[Symbol.iterator]());
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+ var res = (0, pairwise_ts_1.parsePairwiseBlocks)(arr.split('\n')[Symbol.iterator]());
28
28
  if (res === undefined) {
29
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  throw new Error('No blocks parsed');
30
30
  }
31
- const alns = res.seqs.map((n, index) => ({ id: res.ids[index], seq: n }));
32
- const { consensus } = res;
31
+ var alns = res.seqs.map(function (n, index) { return ({ id: res.ids[index], seq: n }); });
32
+ var consensus = res.consensus;
33
33
  if (consensus.length != alns[0].seq.length) {
34
- throw new Error(`Consensus length != sequence length. Con ${consensus.length} seq ${alns[0].seq.length}`);
34
+ throw new Error("Consensus length != sequence length. Con ".concat(consensus.length, " seq ").concat(alns[0].seq.length));
35
35
  }
36
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  if (alns.length !== 2) {
37
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  throw new Error('More than two sequences in pairwise alignment');
38
38
  }
39
39
  return {
40
- consensus,
40
+ consensus: consensus,
41
41
  alns: alns,
42
42
  };
43
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  }
44
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  function parse(contents) {
45
- const iter = contents.split('\n')[Symbol.iterator]();
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+ var iter = contents.split('\n')[Symbol.iterator]();
46
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  return parseClustalIter(iter);
47
47
  }
48
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  function parsePairwise(contents) {
49
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  return parsePairwiseIter(contents
50
50
  .split('\n')
51
- .filter(f => !f.startsWith('#'))
51
+ .filter(function (f) { return !f.startsWith('#'); })
52
52
  .join('\n'));
53
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  }
54
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  //# sourceMappingURL=index.js.map
package/dist/index.js.map CHANGED
@@ -1 +1 @@
1
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1
+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;AAGA,4CAqBC;AAMD,8CAoBC;AAED,sBAGC;AAED,sCAOC;AAhED,6CAAmD;AACnD,qCAA0E;AAE1E,SAAgB,gBAAgB,CAAC,GAAqB;IACpD,IAAM,IAAI,GAAG,IAAA,8BAAoB,EAAC,GAAG,CAAC,CAAA;IACtC,IAAI,CAAC,IAAI,EAAE,CAAC;QACV,MAAM,IAAI,KAAK,CAAC,qBAAqB,CAAC,CAAA;IACxC,CAAC;IACD,IAAM,MAAM,GAAG,IAAA,qBAAW,EAAC,IAAI,CAAC,CAAA;IAEhC,IAAM,GAAG,GAAG,IAAA,qBAAW,EAAC,GAAG,CAAC,CAAA;IAC5B,IAAI,GAAG,KAAK,SAAS,EAAE,CAAC;QACtB,MAAM,IAAI,KAAK,CAAC,kBAAkB,CAAC,CAAA;IACrC,CAAC;IAED,IAAM,IAAI,GAAG,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,UAAC,CAAC,EAAE,KAAK,IAAK,OAAA,CAAC,EAAE,EAAE,EAAE,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,GAAG,EAAE,CAAC,EAAE,CAAC,EAAhC,CAAgC,CAAC,CAAA;IACjE,IAAA,SAAS,GAAK,GAAG,UAAR,CAAQ;IACzB,IAAI,SAAS,CAAC,MAAM,IAAI,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,MAAM,EAAE,CAAC;QAC3C,MAAM,IAAI,KAAK,CACb,mDAA4C,SAAS,CAAC,MAAM,kBAAQ,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,MAAM,CAAE,CACzF,CAAA;IACH,CAAC;IAED,OAAO,EAAE,SAAS,WAAA,EAAE,IAAI,MAAA,EAAE,MAAM,QAAA,EAAE,CAAA;AACpC,CAAC;AAMD,SAAgB,iBAAiB,CAAC,GAAW;IAC3C,IAAM,GAAG,GAAG,IAAA,iCAAmB,EAAC,GAAG,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,MAAM,CAAC,QAAQ,CAAC,EAAE,CAAC,CAAA;IACnE,IAAI,GAAG,KAAK,SAAS,EAAE,CAAC;QACtB,MAAM,IAAI,KAAK,CAAC,kBAAkB,CAAC,CAAA;IACrC,CAAC;IAED,IAAM,IAAI,GAAG,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,UAAC,CAAC,EAAE,KAAK,IAAK,OAAA,CAAC,EAAE,EAAE,EAAE,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,GAAG,EAAE,CAAC,EAAE,CAAC,EAAhC,CAAgC,CAAC,CAAA;IACjE,IAAA,SAAS,GAAK,GAAG,UAAR,CAAQ;IACzB,IAAI,SAAS,CAAC,MAAM,IAAI,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,MAAM,EAAE,CAAC;QAC3C,MAAM,IAAI,KAAK,CACb,mDAA4C,SAAS,CAAC,MAAM,kBAAQ,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,MAAM,CAAE,CACzF,CAAA;IACH,CAAC;IACD,IAAI,IAAI,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACtB,MAAM,IAAI,KAAK,CAAC,+CAA+C,CAAC,CAAA;IAClE,CAAC;IACD,OAAO;QACL,SAAS,WAAA;QACT,IAAI,EAAE,IAAkB;KACzB,CAAA;AACH,CAAC;AAED,SAAgB,KAAK,CAAC,QAAgB;IACpC,IAAM,IAAI,GAAG,QAAQ,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,MAAM,CAAC,QAAQ,CAAC,EAAE,CAAA;IACpD,OAAO,gBAAgB,CAAC,IAAI,CAAC,CAAA;AAC/B,CAAC;AAED,SAAgB,aAAa,CAAC,QAAgB;IAC5C,OAAO,iBAAiB,CACtB,QAAQ;SACL,KAAK,CAAC,IAAI,CAAC;SACX,MAAM,CAAC,UAAA,CAAC,IAAI,OAAA,CAAC,CAAC,CAAC,UAAU,CAAC,GAAG,CAAC,EAAlB,CAAkB,CAAC;SAC/B,IAAI,CAAC,IAAI,CAAC,CACd,CAAA;AACH,CAAC"}
package/dist/package.json ADDED
@@ -0,0 +1 @@
1
+ {"type": "commonjs"}
package/dist/pairwise.d.ts CHANGED
@@ -1,4 +1,4 @@
1
- export declare function getSeqBounds(line: string): readonly [number, number];
1
+ export declare function getSeqBounds(line: string, seqIndex: number): readonly [number, number];
2
2
  export declare function parsePairwiseBlock(arr: Iterator<string>): {
3
3
  ids: string[];
4
4
  seqs: string[];
package/dist/pairwise.js CHANGED
@@ -3,50 +3,60 @@ Object.defineProperty(exports, "__esModule", { value: true });
3
3
  exports.getSeqBounds = getSeqBounds;
4
4
  exports.parsePairwiseBlock = parsePairwiseBlock;
5
5
  exports.parsePairwiseBlocks = parsePairwiseBlocks;
6
- const util_1 = require("./util");
7
- function getSeqBounds(line) {
8
- const fields = line.split(/\s+/);
9
- const k1 = fields[0].length + fields[1].length;
10
- const temp = line.slice(k1);
11
- const s = k1 + temp.indexOf(fields[2]);
12
- const e = s + fields[2].length;
13
- return [s, e];
6
+ var util_ts_1 = require("./util.js");
7
+ function isSequenceLine(line) {
8
+ var trimmed = line.trim();
9
+ return /^\w+\s+/.test(trimmed);
10
+ }
11
+ function hasPositionNumbers(fields) {
12
+ return fields.length >= 3 && /^\d+$/.test(fields[1]);
13
+ }
14
+ function getSeqBounds(line, seqIndex) {
15
+ var trimmed = line.trim();
16
+ var fields = trimmed.split(/\s+/);
17
+ var seq = fields[seqIndex];
18
+ var seqStart = line.indexOf(seq, line.indexOf(fields[0]) + fields[0].length);
19
+ return [seqStart, seqStart + seq.length];
14
20
  }
15
21
  // Use the first block to get the sequence identifiers
16
22
  function parsePairwiseBlock(arr) {
17
- let line = (0, util_1.getFirstNonEmptyLine)(arr);
18
- const block = [];
19
- let consensusLine = '';
23
+ var line = (0, util_ts_1.getFirstNonEmptyLine)(arr);
24
+ var block = [];
25
+ var consensusLine = '';
20
26
  if (!line) {
21
27
  return undefined;
22
28
  }
23
29
  while (line) {
24
- if (line.startsWith(' ')) {
25
- consensusLine = line;
30
+ if (isSequenceLine(line)) {
31
+ block.push(line);
26
32
  }
27
33
  else {
28
- block.push(line);
34
+ consensusLine = line;
29
35
  }
30
36
  line = arr.next().value;
31
37
  }
32
- const [start, end] = getSeqBounds(block[0]);
33
- const fields = block.map(s => s.split(/\s+/));
34
- const ids = fields.map(s => s[0]);
35
- const seqs = fields.map(s => s[2]);
36
- let consensus = consensusLine.slice(start, end);
38
+ if (block.length === 0) {
39
+ return undefined;
40
+ }
41
+ var fields = block.map(function (s) { return s.trim().split(/\s+/); });
42
+ var seqIndex = hasPositionNumbers(fields[0]) ? 2 : 1;
43
+ var _a = getSeqBounds(block[0], seqIndex), start = _a[0], end = _a[1];
44
+ var ids = fields.map(function (s) { return s[0]; });
45
+ var seqs = fields.map(function (s) { return s[seqIndex]; });
46
+ var consensus = consensusLine.slice(start, end);
37
47
  // handle if the consensus trailing whitespace got trimmed
38
- const remainder = seqs[0].length - consensus.length;
39
- if (remainder) {
48
+ var remainder = seqs[0].length - consensus.length;
49
+ if (remainder > 0) {
40
50
  consensus += ' '.repeat(remainder);
41
51
  }
42
- return { ids, seqs, consensus };
52
+ return { ids: ids, seqs: seqs, consensus: consensus };
43
53
  }
44
54
  function parsePairwiseBlocks(arr) {
45
- let block;
46
- const res = parsePairwiseBlock(arr);
55
+ var block;
56
+ var res = parsePairwiseBlock(arr);
47
57
  if (res !== undefined) {
48
58
  while ((block = parsePairwiseBlock(arr))) {
49
- for (let i = 0; i < block.seqs.length; i++) {
59
+ for (var i = 0; i < block.seqs.length; i++) {
50
60
  res.seqs[i] += block.seqs[i];
51
61
  }
52
62
  res.consensus += block.consensus;
package/dist/pairwise.js.map CHANGED
@@ -1 +1 @@
1
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1
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package/dist/util.js CHANGED
@@ -7,37 +7,37 @@ exports.getSeqBounds = getSeqBounds;
7
7
  exports.parseBlock = parseBlock;
8
8
  exports.parseBlocks = parseBlocks;
9
9
  function parseVersion(line) {
10
- const res = /\(?(\d+(\.\d+)+)\)?/.exec(line);
10
+ var res = /\(?(\d+(\.\d+)+)\)?/.exec(line);
11
11
  return res && res.length > 1 ? res[1] : '';
12
12
  }
13
13
  function parseHeader(info) {
14
- const knownHeaders = ['CLUSTAL', 'PROBCONS', 'MUSCLE', 'MSAPROBS', 'Kalign'];
15
- if (!knownHeaders.some(l => info.startsWith(l))) {
16
- console.warn(`${info} is not a known CLUSTAL header: ${knownHeaders.join(',')}, proceeding but could indicate an issue`);
14
+ var knownHeaders = ['CLUSTAL', 'PROBCONS', 'MUSCLE', 'MSAPROBS', 'Kalign'];
15
+ if (!knownHeaders.some(function (l) { return info.startsWith(l); })) {
16
+ console.warn("".concat(info, " is not a known CLUSTAL header: ").concat(knownHeaders.join(','), ", proceeding but could indicate an issue"));
17
17
  }
18
- const version = parseVersion(info);
19
- return { info, version };
18
+ var version = parseVersion(info);
19
+ return { info: info, version: version };
20
20
  }
21
21
  function getFirstNonEmptyLine(arr) {
22
22
  // There should be two blank lines after the header line
23
- let line = arr.next();
23
+ var line = arr.next();
24
24
  while (!line.done && line.value.trim() === '') {
25
25
  line = arr.next();
26
26
  }
27
27
  return line.value;
28
28
  }
29
29
  function getSeqBounds(line) {
30
- const fields = line.split(/\s+/);
31
- const temp = line.slice(fields[0].length);
32
- const s = fields[0].length + temp.indexOf(fields[1]);
33
- const e = s + fields[1].length;
30
+ var fields = line.split(/\s+/);
31
+ var temp = line.slice(fields[0].length);
32
+ var s = fields[0].length + temp.indexOf(fields[1]);
33
+ var e = s + fields[1].length;
34
34
  return [s, e];
35
35
  }
36
36
  // Use the first block to get the sequence identifiers
37
37
  function parseBlock(arr) {
38
- let line = getFirstNonEmptyLine(arr);
39
- const block = [];
40
- let consensusLine = '';
38
+ var line = getFirstNonEmptyLine(arr);
39
+ var block = [];
40
+ var consensusLine = '';
41
41
  if (!line) {
42
42
  return undefined;
43
43
  }
@@ -50,24 +50,24 @@ function parseBlock(arr) {
50
50
  }
51
51
  line = arr.next().value;
52
52
  }
53
- const [start, end] = getSeqBounds(block[0]);
54
- const fields = block.map(s => s.split(/\s+/));
55
- const ids = fields.map(s => s[0]);
56
- const seqs = block.map(s => s.slice(start, end));
57
- let consensus = consensusLine.slice(start, end);
53
+ var _a = getSeqBounds(block[0]), start = _a[0], end = _a[1];
54
+ var fields = block.map(function (s) { return s.split(/\s+/); });
55
+ var ids = fields.map(function (s) { return s[0]; });
56
+ var seqs = block.map(function (s) { return s.slice(start, end); });
57
+ var consensus = consensusLine.slice(start, end);
58
58
  // handle if the consensus trailing whitespace got trimmed
59
- const remainder = seqs[0].length - consensus.length;
59
+ var remainder = seqs[0].length - consensus.length;
60
60
  if (remainder) {
61
61
  consensus += ' '.repeat(remainder);
62
62
  }
63
- return { ids, seqs, consensus };
63
+ return { ids: ids, seqs: seqs, consensus: consensus };
64
64
  }
65
65
  function parseBlocks(arr) {
66
- let block;
67
- const res = parseBlock(arr);
66
+ var block;
67
+ var res = parseBlock(arr);
68
68
  if (res !== undefined) {
69
69
  while ((block = parseBlock(arr))) {
70
- for (let i = 0; i < block.seqs.length; i++) {
70
+ for (var i = 0; i < block.seqs.length; i++) {
71
71
  res.seqs[i] += block.seqs[i];
72
72
  }
73
73
  res.consensus += block.consensus;
package/dist/util.js.map CHANGED
@@ -1 +1 @@
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package/esm/index.js CHANGED
@@ -1,48 +1,54 @@
1
- import { parsePairwiseBlocks } from './pairwise';
2
- import { parseBlocks, parseHeader, getFirstNonEmptyLine } from './util';
3
- export function parseClustalIter(arr) {
4
- const line = getFirstNonEmptyLine(arr);
1
+ "use strict";
2
+ Object.defineProperty(exports, "__esModule", { value: true });
3
+ exports.parseClustalIter = parseClustalIter;
4
+ exports.parsePairwiseIter = parsePairwiseIter;
5
+ exports.parse = parse;
6
+ exports.parsePairwise = parsePairwise;
7
+ var pairwise_ts_1 = require("./pairwise.js");
8
+ var util_ts_1 = require("./util.js");
9
+ function parseClustalIter(arr) {
10
+ var line = (0, util_ts_1.getFirstNonEmptyLine)(arr);
5
11
  if (!line) {
6
12
  throw new Error('Empty file received');
7
13
  }
8
- const header = parseHeader(line);
9
- const res = parseBlocks(arr);
14
+ var header = (0, util_ts_1.parseHeader)(line);
15
+ var res = (0, util_ts_1.parseBlocks)(arr);
10
16
  if (res === undefined) {
11
17
  throw new Error('No blocks parsed');
12
18
  }
13
- const alns = res.seqs.map((n, index) => ({ id: res.ids[index], seq: n }));
14
- const { consensus } = res;
19
+ var alns = res.seqs.map(function (n, index) { return ({ id: res.ids[index], seq: n }); });
20
+ var consensus = res.consensus;
15
21
  if (consensus.length != alns[0].seq.length) {
16
- throw new Error(`Consensus length != sequence length. Con ${consensus.length} seq ${alns[0].seq.length}`);
22
+ throw new Error("Consensus length != sequence length. Con ".concat(consensus.length, " seq ").concat(alns[0].seq.length));
17
23
  }
18
- return { consensus, alns, header };
24
+ return { consensus: consensus, alns: alns, header: header };
19
25
  }
20
- export function parsePairwiseIter(arr) {
21
- const res = parsePairwiseBlocks(arr.split('\n')[Symbol.iterator]());
26
+ function parsePairwiseIter(arr) {
27
+ var res = (0, pairwise_ts_1.parsePairwiseBlocks)(arr.split('\n')[Symbol.iterator]());
22
28
  if (res === undefined) {
23
29
  throw new Error('No blocks parsed');
24
30
  }
25
- const alns = res.seqs.map((n, index) => ({ id: res.ids[index], seq: n }));
26
- const { consensus } = res;
31
+ var alns = res.seqs.map(function (n, index) { return ({ id: res.ids[index], seq: n }); });
32
+ var consensus = res.consensus;
27
33
  if (consensus.length != alns[0].seq.length) {
28
- throw new Error(`Consensus length != sequence length. Con ${consensus.length} seq ${alns[0].seq.length}`);
34
+ throw new Error("Consensus length != sequence length. Con ".concat(consensus.length, " seq ").concat(alns[0].seq.length));
29
35
  }
30
36
  if (alns.length !== 2) {
31
37
  throw new Error('More than two sequences in pairwise alignment');
32
38
  }
33
39
  return {
34
- consensus,
40
+ consensus: consensus,
35
41
  alns: alns,
36
42
  };
37
43
  }
38
- export function parse(contents) {
39
- const iter = contents.split('\n')[Symbol.iterator]();
44
+ function parse(contents) {
45
+ var iter = contents.split('\n')[Symbol.iterator]();
40
46
  return parseClustalIter(iter);
41
47
  }
42
- export function parsePairwise(contents) {
48
+ function parsePairwise(contents) {
43
49
  return parsePairwiseIter(contents
44
50
  .split('\n')
45
- .filter(f => !f.startsWith('#'))
51
+ .filter(function (f) { return !f.startsWith('#'); })
46
52
  .join('\n'));
47
53
  }
48
54
  //# sourceMappingURL=index.js.map
package/esm/index.js.map CHANGED
@@ -1 +1 @@
1
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+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;AAGA,4CAqBC;AAMD,8CAoBC;AAED,sBAGC;AAED,sCAOC;AAhED,6CAAmD;AACnD,qCAA0E;AAE1E,SAAgB,gBAAgB,CAAC,GAAqB;IACpD,IAAM,IAAI,GAAG,IAAA,8BAAoB,EAAC,GAAG,CAAC,CAAA;IACtC,IAAI,CAAC,IAAI,EAAE,CAAC;QACV,MAAM,IAAI,KAAK,CAAC,qBAAqB,CAAC,CAAA;IACxC,CAAC;IACD,IAAM,MAAM,GAAG,IAAA,qBAAW,EAAC,IAAI,CAAC,CAAA;IAEhC,IAAM,GAAG,GAAG,IAAA,qBAAW,EAAC,GAAG,CAAC,CAAA;IAC5B,IAAI,GAAG,KAAK,SAAS,EAAE,CAAC;QACtB,MAAM,IAAI,KAAK,CAAC,kBAAkB,CAAC,CAAA;IACrC,CAAC;IAED,IAAM,IAAI,GAAG,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,UAAC,CAAC,EAAE,KAAK,IAAK,OAAA,CAAC,EAAE,EAAE,EAAE,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,GAAG,EAAE,CAAC,EAAE,CAAC,EAAhC,CAAgC,CAAC,CAAA;IACjE,IAAA,SAAS,GAAK,GAAG,UAAR,CAAQ;IACzB,IAAI,SAAS,CAAC,MAAM,IAAI,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,MAAM,EAAE,CAAC;QAC3C,MAAM,IAAI,KAAK,CACb,mDAA4C,SAAS,CAAC,MAAM,kBAAQ,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,MAAM,CAAE,CACzF,CAAA;IACH,CAAC;IAED,OAAO,EAAE,SAAS,WAAA,EAAE,IAAI,MAAA,EAAE,MAAM,QAAA,EAAE,CAAA;AACpC,CAAC;AAMD,SAAgB,iBAAiB,CAAC,GAAW;IAC3C,IAAM,GAAG,GAAG,IAAA,iCAAmB,EAAC,GAAG,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,MAAM,CAAC,QAAQ,CAAC,EAAE,CAAC,CAAA;IACnE,IAAI,GAAG,KAAK,SAAS,EAAE,CAAC;QACtB,MAAM,IAAI,KAAK,CAAC,kBAAkB,CAAC,CAAA;IACrC,CAAC;IAED,IAAM,IAAI,GAAG,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,UAAC,CAAC,EAAE,KAAK,IAAK,OAAA,CAAC,EAAE,EAAE,EAAE,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,GAAG,EAAE,CAAC,EAAE,CAAC,EAAhC,CAAgC,CAAC,CAAA;IACjE,IAAA,SAAS,GAAK,GAAG,UAAR,CAAQ;IACzB,IAAI,SAAS,CAAC,MAAM,IAAI,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,MAAM,EAAE,CAAC;QAC3C,MAAM,IAAI,KAAK,CACb,mDAA4C,SAAS,CAAC,MAAM,kBAAQ,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,MAAM,CAAE,CACzF,CAAA;IACH,CAAC;IACD,IAAI,IAAI,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACtB,MAAM,IAAI,KAAK,CAAC,+CAA+C,CAAC,CAAA;IAClE,CAAC;IACD,OAAO;QACL,SAAS,WAAA;QACT,IAAI,EAAE,IAAkB;KACzB,CAAA;AACH,CAAC;AAED,SAAgB,KAAK,CAAC,QAAgB;IACpC,IAAM,IAAI,GAAG,QAAQ,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,MAAM,CAAC,QAAQ,CAAC,EAAE,CAAA;IACpD,OAAO,gBAAgB,CAAC,IAAI,CAAC,CAAA;AAC/B,CAAC;AAED,SAAgB,aAAa,CAAC,QAAgB;IAC5C,OAAO,iBAAiB,CACtB,QAAQ;SACL,KAAK,CAAC,IAAI,CAAC;SACX,MAAM,CAAC,UAAA,CAAC,IAAI,OAAA,CAAC,CAAC,CAAC,UAAU,CAAC,GAAG,CAAC,EAAlB,CAAkB,CAAC;SAC/B,IAAI,CAAC,IAAI,CAAC,CACd,CAAA;AACH,CAAC"}
package/esm/pairwise.d.ts CHANGED
@@ -1,4 +1,4 @@
1
- export declare function getSeqBounds(line: string): readonly [number, number];
1
+ export declare function getSeqBounds(line: string, seqIndex: number): readonly [number, number];
2
2
  export declare function parsePairwiseBlock(arr: Iterator<string>): {
3
3
  ids: string[];
4
4
  seqs: string[];
package/esm/pairwise.js CHANGED
@@ -1,47 +1,62 @@
1
- import { getFirstNonEmptyLine } from './util';
2
- export function getSeqBounds(line) {
3
- const fields = line.split(/\s+/);
4
- const k1 = fields[0].length + fields[1].length;
5
- const temp = line.slice(k1);
6
- const s = k1 + temp.indexOf(fields[2]);
7
- const e = s + fields[2].length;
8
- return [s, e];
1
+ "use strict";
2
+ Object.defineProperty(exports, "__esModule", { value: true });
3
+ exports.getSeqBounds = getSeqBounds;
4
+ exports.parsePairwiseBlock = parsePairwiseBlock;
5
+ exports.parsePairwiseBlocks = parsePairwiseBlocks;
6
+ var util_ts_1 = require("./util.js");
7
+ function isSequenceLine(line) {
8
+ var trimmed = line.trim();
9
+ return /^\w+\s+/.test(trimmed);
10
+ }
11
+ function hasPositionNumbers(fields) {
12
+ return fields.length >= 3 && /^\d+$/.test(fields[1]);
13
+ }
14
+ function getSeqBounds(line, seqIndex) {
15
+ var trimmed = line.trim();
16
+ var fields = trimmed.split(/\s+/);
17
+ var seq = fields[seqIndex];
18
+ var seqStart = line.indexOf(seq, line.indexOf(fields[0]) + fields[0].length);
19
+ return [seqStart, seqStart + seq.length];
9
20
  }
10
21
  // Use the first block to get the sequence identifiers
11
- export function parsePairwiseBlock(arr) {
12
- let line = getFirstNonEmptyLine(arr);
13
- const block = [];
14
- let consensusLine = '';
22
+ function parsePairwiseBlock(arr) {
23
+ var line = (0, util_ts_1.getFirstNonEmptyLine)(arr);
24
+ var block = [];
25
+ var consensusLine = '';
15
26
  if (!line) {
16
27
  return undefined;
17
28
  }
18
29
  while (line) {
19
- if (line.startsWith(' ')) {
20
- consensusLine = line;
30
+ if (isSequenceLine(line)) {
31
+ block.push(line);
21
32
  }
22
33
  else {
23
- block.push(line);
34
+ consensusLine = line;
24
35
  }
25
36
  line = arr.next().value;
26
37
  }
27
- const [start, end] = getSeqBounds(block[0]);
28
- const fields = block.map(s => s.split(/\s+/));
29
- const ids = fields.map(s => s[0]);
30
- const seqs = fields.map(s => s[2]);
31
- let consensus = consensusLine.slice(start, end);
38
+ if (block.length === 0) {
39
+ return undefined;
40
+ }
41
+ var fields = block.map(function (s) { return s.trim().split(/\s+/); });
42
+ var seqIndex = hasPositionNumbers(fields[0]) ? 2 : 1;
43
+ var _a = getSeqBounds(block[0], seqIndex), start = _a[0], end = _a[1];
44
+ var ids = fields.map(function (s) { return s[0]; });
45
+ var seqs = fields.map(function (s) { return s[seqIndex]; });
46
+ var consensus = consensusLine.slice(start, end);
32
47
  // handle if the consensus trailing whitespace got trimmed
33
- const remainder = seqs[0].length - consensus.length;
34
- if (remainder) {
48
+ var remainder = seqs[0].length - consensus.length;
49
+ if (remainder > 0) {
35
50
  consensus += ' '.repeat(remainder);
36
51
  }
37
- return { ids, seqs, consensus };
52
+ return { ids: ids, seqs: seqs, consensus: consensus };
38
53
  }
39
- export function parsePairwiseBlocks(arr) {
40
- let block;
41
- const res = parsePairwiseBlock(arr);
54
+ function parsePairwiseBlocks(arr) {
55
+ var block;
56
+ var res = parsePairwiseBlock(arr);
42
57
  if (res !== undefined) {
43
58
  while ((block = parsePairwiseBlock(arr))) {
44
- for (let i = 0; i < block.seqs.length; i++) {
59
+ for (var i = 0; i < block.seqs.length; i++) {
45
60
  res.seqs[i] += block.seqs[i];
46
61
  }
47
62
  res.consensus += block.consensus;
package/esm/pairwise.js.map CHANGED
@@ -1 +1 @@
1
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1
+ {"version":3,"file":"pairwise.js","sourceRoot":"","sources":["../src/pairwise.ts"],"names":[],"mappings":";;AAWA,oCAMC;AAGD,gDAkCC;AAED,kDAYC;AApED,qCAAgD;AAEhD,SAAS,cAAc,CAAC,IAAY;IAClC,IAAM,OAAO,GAAG,IAAI,CAAC,IAAI,EAAE,CAAA;IAC3B,OAAO,SAAS,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;AAChC,CAAC;AAED,SAAS,kBAAkB,CAAC,MAAgB;IAC1C,OAAO,MAAM,CAAC,MAAM,IAAI,CAAC,IAAI,OAAO,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAA;AACtD,CAAC;AAED,SAAgB,YAAY,CAAC,IAAY,EAAE,QAAgB;IACzD,IAAM,OAAO,GAAG,IAAI,CAAC,IAAI,EAAE,CAAA;IAC3B,IAAM,MAAM,GAAG,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,CAAA;IACnC,IAAM,GAAG,GAAG,MAAM,CAAC,QAAQ,CAAC,CAAA;IAC5B,IAAM,QAAQ,GAAG,IAAI,CAAC,OAAO,CAAC,GAAG,EAAE,IAAI,CAAC,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,GAAG,MAAM,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAA;IAC9E,OAAO,CAAC,QAAQ,EAAE,QAAQ,GAAG,GAAG,CAAC,MAAM,CAAU,CAAA;AACnD,CAAC;AAED,sDAAsD;AACtD,SAAgB,kBAAkB,CAAC,GAAqB;IACtD,IAAI,IAAI,GAAG,IAAA,8BAAoB,EAAC,GAAG,CAAC,CAAA;IACpC,IAAM,KAAK,GAAa,EAAE,CAAA;IAC1B,IAAI,aAAa,GAAG,EAAE,CAAA;IACtB,IAAI,CAAC,IAAI,EAAE,CAAC;QACV,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,OAAO,IAAI,EAAE,CAAC;QACZ,IAAI,cAAc,CAAC,IAAI,CAAC,EAAE,CAAC;YACzB,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QAClB,CAAC;aAAM,CAAC;YACN,aAAa,GAAG,IAAI,CAAA;QACtB,CAAC;QACD,IAAI,GAAG,GAAG,CAAC,IAAI,EAAE,CAAC,KAAK,CAAA;IACzB,CAAC;IAED,IAAI,KAAK,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACvB,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,IAAM,MAAM,GAAG,KAAK,CAAC,GAAG,CAAC,UAAA,CAAC,IAAI,OAAA,CAAC,CAAC,IAAI,EAAE,CAAC,KAAK,CAAC,KAAK,CAAC,EAArB,CAAqB,CAAC,CAAA;IACpD,IAAM,QAAQ,GAAG,kBAAkB,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAChD,IAAA,KAAe,YAAY,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,QAAQ,CAAC,EAA9C,KAAK,QAAA,EAAE,GAAG,QAAoC,CAAA;IACrD,IAAM,GAAG,GAAG,MAAM,CAAC,GAAG,CAAC,UAAA,CAAC,IAAI,OAAA,CAAC,CAAC,CAAC,CAAC,EAAJ,CAAI,CAAC,CAAA;IACjC,IAAM,IAAI,GAAG,MAAM,CAAC,GAAG,CAAC,UAAA,CAAC,IAAI,OAAA,CAAC,CAAC,QAAQ,CAAC,EAAX,CAAW,CAAC,CAAA;IACzC,IAAI,SAAS,GAAG,aAAa,CAAC,KAAK,CAAC,KAAK,EAAE,GAAG,CAAC,CAAA;IAE/C,0DAA0D;IAC1D,IAAM,SAAS,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC,MAAM,GAAG,SAAS,CAAC,MAAM,CAAA;IACnD,IAAI,SAAS,GAAG,CAAC,EAAE,CAAC;QAClB,SAAS,IAAI,GAAG,CAAC,MAAM,CAAC,SAAS,CAAC,CAAA;IACpC,CAAC;IACD,OAAO,EAAE,GAAG,KAAA,EAAE,IAAI,MAAA,EAAE,SAAS,WAAA,EAAE,CAAA;AACjC,CAAC;AAED,SAAgB,mBAAmB,CAAC,GAAqB;IACvD,IAAI,KAAK,CAAA;IACT,IAAM,GAAG,GAAG,kBAAkB,CAAC,GAAG,CAAC,CAAA;IACnC,IAAI,GAAG,KAAK,SAAS,EAAE,CAAC;QACtB,OAAO,CAAC,KAAK,GAAG,kBAAkB,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC;YACzC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;gBAC3C,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC,IAAI,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;YAC9B,CAAC;YACD,GAAG,CAAC,SAAS,IAAI,KAAK,CAAC,SAAS,CAAA;QAClC,CAAC;IACH,CAAC;IACD,OAAO,GAAG,CAAA;AACZ,CAAC"}
package/esm/util.js CHANGED
@@ -1,35 +1,43 @@
1
- export function parseVersion(line) {
2
- const res = /\(?(\d+(\.\d+)+)\)?/.exec(line);
1
+ "use strict";
2
+ Object.defineProperty(exports, "__esModule", { value: true });
3
+ exports.parseVersion = parseVersion;
4
+ exports.parseHeader = parseHeader;
5
+ exports.getFirstNonEmptyLine = getFirstNonEmptyLine;
6
+ exports.getSeqBounds = getSeqBounds;
7
+ exports.parseBlock = parseBlock;
8
+ exports.parseBlocks = parseBlocks;
9
+ function parseVersion(line) {
10
+ var res = /\(?(\d+(\.\d+)+)\)?/.exec(line);
3
11
  return res && res.length > 1 ? res[1] : '';
4
12
  }
5
- export function parseHeader(info) {
6
- const knownHeaders = ['CLUSTAL', 'PROBCONS', 'MUSCLE', 'MSAPROBS', 'Kalign'];
7
- if (!knownHeaders.some(l => info.startsWith(l))) {
8
- console.warn(`${info} is not a known CLUSTAL header: ${knownHeaders.join(',')}, proceeding but could indicate an issue`);
13
+ function parseHeader(info) {
14
+ var knownHeaders = ['CLUSTAL', 'PROBCONS', 'MUSCLE', 'MSAPROBS', 'Kalign'];
15
+ if (!knownHeaders.some(function (l) { return info.startsWith(l); })) {
16
+ console.warn("".concat(info, " is not a known CLUSTAL header: ").concat(knownHeaders.join(','), ", proceeding but could indicate an issue"));
9
17
  }
10
- const version = parseVersion(info);
11
- return { info, version };
18
+ var version = parseVersion(info);
19
+ return { info: info, version: version };
12
20
  }
13
- export function getFirstNonEmptyLine(arr) {
21
+ function getFirstNonEmptyLine(arr) {
14
22
  // There should be two blank lines after the header line
15
- let line = arr.next();
23
+ var line = arr.next();
16
24
  while (!line.done && line.value.trim() === '') {
17
25
  line = arr.next();
18
26
  }
19
27
  return line.value;
20
28
  }
21
- export function getSeqBounds(line) {
22
- const fields = line.split(/\s+/);
23
- const temp = line.slice(fields[0].length);
24
- const s = fields[0].length + temp.indexOf(fields[1]);
25
- const e = s + fields[1].length;
29
+ function getSeqBounds(line) {
30
+ var fields = line.split(/\s+/);
31
+ var temp = line.slice(fields[0].length);
32
+ var s = fields[0].length + temp.indexOf(fields[1]);
33
+ var e = s + fields[1].length;
26
34
  return [s, e];
27
35
  }
28
36
  // Use the first block to get the sequence identifiers
29
- export function parseBlock(arr) {
30
- let line = getFirstNonEmptyLine(arr);
31
- const block = [];
32
- let consensusLine = '';
37
+ function parseBlock(arr) {
38
+ var line = getFirstNonEmptyLine(arr);
39
+ var block = [];
40
+ var consensusLine = '';
33
41
  if (!line) {
34
42
  return undefined;
35
43
  }
@@ -42,24 +50,24 @@ export function parseBlock(arr) {
42
50
  }
43
51
  line = arr.next().value;
44
52
  }
45
- const [start, end] = getSeqBounds(block[0]);
46
- const fields = block.map(s => s.split(/\s+/));
47
- const ids = fields.map(s => s[0]);
48
- const seqs = block.map(s => s.slice(start, end));
49
- let consensus = consensusLine.slice(start, end);
53
+ var _a = getSeqBounds(block[0]), start = _a[0], end = _a[1];
54
+ var fields = block.map(function (s) { return s.split(/\s+/); });
55
+ var ids = fields.map(function (s) { return s[0]; });
56
+ var seqs = block.map(function (s) { return s.slice(start, end); });
57
+ var consensus = consensusLine.slice(start, end);
50
58
  // handle if the consensus trailing whitespace got trimmed
51
- const remainder = seqs[0].length - consensus.length;
59
+ var remainder = seqs[0].length - consensus.length;
52
60
  if (remainder) {
53
61
  consensus += ' '.repeat(remainder);
54
62
  }
55
- return { ids, seqs, consensus };
63
+ return { ids: ids, seqs: seqs, consensus: consensus };
56
64
  }
57
- export function parseBlocks(arr) {
58
- let block;
59
- const res = parseBlock(arr);
65
+ function parseBlocks(arr) {
66
+ var block;
67
+ var res = parseBlock(arr);
60
68
  if (res !== undefined) {
61
69
  while ((block = parseBlock(arr))) {
62
- for (let i = 0; i < block.seqs.length; i++) {
70
+ for (var i = 0; i < block.seqs.length; i++) {
63
71
  res.seqs[i] += block.seqs[i];
64
72
  }
65
73
  res.consensus += block.consensus;
package/esm/util.js.map CHANGED
@@ -1 +1 @@
1
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1
+ {"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":";;AAAA,oCAGC;AACD,kCAYC;AAED,oDAOC;AAED,oCAMC;AAGD,gCA4BC;AAED,kCAYC;AA9ED,SAAgB,YAAY,CAAC,IAAY;IACvC,IAAM,GAAG,GAAG,qBAAqB,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;IAC5C,OAAO,GAAG,IAAI,GAAG,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAA;AAC5C,CAAC;AACD,SAAgB,WAAW,CAAC,IAAY;IACtC,IAAM,YAAY,GAAG,CAAC,SAAS,EAAE,UAAU,EAAE,QAAQ,EAAE,UAAU,EAAE,QAAQ,CAAC,CAAA;IAE5E,IAAI,CAAC,YAAY,CAAC,IAAI,CAAC,UAAA,CAAC,IAAI,OAAA,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,EAAlB,CAAkB,CAAC,EAAE,CAAC;QAChD,OAAO,CAAC,IAAI,CACV,UAAG,IAAI,6CAAmC,YAAY,CAAC,IAAI,CACzD,GAAG,CACJ,6CAA0C,CAC5C,CAAA;IACH,CAAC;IACD,IAAM,OAAO,GAAG,YAAY,CAAC,IAAI,CAAC,CAAA;IAClC,OAAO,EAAE,IAAI,MAAA,EAAE,OAAO,SAAA,EAAE,CAAA;AAC1B,CAAC;AAED,SAAgB,oBAAoB,CAAC,GAAqB;IACxD,wDAAwD;IACxD,IAAI,IAAI,GAAG,GAAG,CAAC,IAAI,EAAE,CAAA;IACrB,OAAO,CAAC,IAAI,CAAC,IAAI,IAAI,IAAI,CAAC,KAAK,CAAC,IAAI,EAAE,KAAK,EAAE,EAAE,CAAC;QAC9C,IAAI,GAAG,GAAG,CAAC,IAAI,EAAE,CAAA;IACnB,CAAC;IACD,OAAO,IAAI,CAAC,KAAK,CAAA;AACnB,CAAC;AAED,SAAgB,YAAY,CAAC,IAAY;IACvC,IAAM,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,KAAK,CAAC,CAAA;IAChC,IAAM,IAAI,GAAG,IAAI,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAA;IACzC,IAAM,CAAC,GAAG,MAAM,CAAC,CAAC,CAAC,CAAC,MAAM,GAAG,IAAI,CAAC,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAA;IACpD,IAAM,CAAC,GAAG,CAAC,GAAG,MAAM,CAAC,CAAC,CAAC,CAAC,MAAM,CAAA;IAC9B,OAAO,CAAC,CAAC,EAAE,CAAC,CAAU,CAAA;AACxB,CAAC;AAED,sDAAsD;AACtD,SAAgB,UAAU,CAAC,GAAqB;IAC9C,IAAI,IAAI,GAAG,oBAAoB,CAAC,GAAG,CAAC,CAAA;IACpC,IAAM,KAAK,GAAG,EAAE,CAAA;IAChB,IAAI,aAAa,GAAG,EAAE,CAAA;IACtB,IAAI,CAAC,IAAI,EAAE,CAAC;QACV,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,OAAO,IAAI,EAAE,CAAC;QACZ,IAAI,IAAI,CAAC,CAAC,CAAC,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE,CAAC;YAC5B,aAAa,GAAG,IAAI,CAAA;QACtB,CAAC;aAAM,CAAC;YACN,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QAClB,CAAC;QACD,IAAI,GAAG,GAAG,CAAC,IAAI,EAAE,CAAC,KAAK,CAAA;IACzB,CAAC;IACK,IAAA,KAAe,YAAY,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,EAApC,KAAK,QAAA,EAAE,GAAG,QAA0B,CAAA;IAC3C,IAAM,MAAM,GAAG,KAAK,CAAC,GAAG,CAAC,UAAA,CAAC,IAAI,OAAA,CAAC,CAAC,KAAK,CAAC,KAAK,CAAC,EAAd,CAAc,CAAC,CAAA;IAC7C,IAAM,GAAG,GAAG,MAAM,CAAC,GAAG,CAAC,UAAA,CAAC,IAAI,OAAA,CAAC,CAAC,CAAC,CAAC,EAAJ,CAAI,CAAC,CAAA;IACjC,IAAM,IAAI,GAAG,KAAK,CAAC,GAAG,CAAC,UAAA,CAAC,IAAI,OAAA,CAAC,CAAC,KAAK,CAAC,KAAK,EAAE,GAAG,CAAC,EAAnB,CAAmB,CAAC,CAAA;IAChD,IAAI,SAAS,GAAG,aAAa,CAAC,KAAK,CAAC,KAAK,EAAE,GAAG,CAAC,CAAA;IAE/C,0DAA0D;IAC1D,IAAM,SAAS,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC,MAAM,GAAG,SAAS,CAAC,MAAM,CAAA;IACnD,IAAI,SAAS,EAAE,CAAC;QACd,SAAS,IAAI,GAAG,CAAC,MAAM,CAAC,SAAS,CAAC,CAAA;IACpC,CAAC;IACD,OAAO,EAAE,GAAG,KAAA,EAAE,IAAI,MAAA,EAAE,SAAS,WAAA,EAAE,CAAA;AACjC,CAAC;AAED,SAAgB,WAAW,CAAC,GAAqB;IAC/C,IAAI,KAAK,CAAA;IACT,IAAM,GAAG,GAAG,UAAU,CAAC,GAAG,CAAC,CAAA;IAC3B,IAAI,GAAG,KAAK,SAAS,EAAE,CAAC;QACtB,OAAO,CAAC,KAAK,GAAG,UAAU,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC;YACjC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;gBAC3C,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC,IAAI,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;YAC9B,CAAC;YACD,GAAG,CAAC,SAAS,IAAI,KAAK,CAAC,SAAS,CAAA;QAClC,CAAC;IACH,CAAC;IACD,OAAO,GAAG,CAAA;AACZ,CAAC"}
package/package.json CHANGED
@@ -1,8 +1,16 @@
1
1
  {
2
2
  "name": "clustal-js",
3
- "version": "2.0.6",
4
- "main": "dist/index.js",
5
- "module": "esm/index.js",
3
+ "version": "2.0.7",
4
+ "type": "module",
5
+ "types": "./dist/index.d.ts",
6
+ "exports": {
7
+ "import": {
8
+ "import": "./esm/index.js"
9
+ },
10
+ "require": {
11
+ "require": "./dist/index.js"
12
+ }
13
+ },
6
14
  "repository": "cmdcolin/clustal-js",
7
15
  "files": [
8
16
  "dist",
@@ -12,25 +20,26 @@
12
20
  "license": "MIT",
13
21
  "devDependencies": {
14
22
  "@types/node": "^22.0.0",
15
- "@typescript-eslint/eslint-plugin": "^8.1.0",
16
- "@typescript-eslint/parser": "^8.1.0",
17
23
  "eslint": "^9.9.0",
18
- "eslint-plugin-unicorn": "^55.0.0",
24
+ "eslint-plugin-import": "^2.32.0",
25
+ "eslint-plugin-unicorn": "^62.0.0",
19
26
  "prettier": "^3.2.5",
20
27
  "rimraf": "^6.0.1",
21
28
  "typescript": "^5.3.3",
22
29
  "typescript-eslint": "^8.1.0",
23
- "vitest": "^2.0.5"
30
+ "vitest": "^4.0.16"
24
31
  },
25
32
  "scripts": {
26
33
  "clean": "rimraf dist esm",
27
- "test": "vitest run",
34
+ "test": "vitest",
28
35
  "lint": "eslint --report-unused-disable-directives --max-warnings 0",
29
- "build": "npm run build:esm && npm run build:es5",
30
- "build:esm": "tsc --target es2018 --outDir esm",
31
- "build:es5": "tsc --target es2015 --module commonjs --outDir dist",
32
- "prebuild": "npm run clean",
33
- "preversion": "npm run lint && npm test && npm run build",
36
+ "format": "prettier --write .",
37
+ "build:esm": "tsc --outDir esm",
38
+ "build:es5": "tsc --module commonjs --outDir dist",
39
+ "build": "yarn build:esm && yarn build:es5",
40
+ "prebuild": "yarn clean",
41
+ "postbuild:es5": "echo '{\"type\": \"commonjs\"}' > dist/package.json",
42
+ "preversion": "yarn lint && yarn test --run && yarn build",
34
43
  "postversion": "git push --follow-tags"
35
44
  }
36
45
  }
package/src/index.ts CHANGED
@@ -1,5 +1,5 @@
1
- import { parsePairwiseBlocks } from './pairwise'
2
- import { parseBlocks, parseHeader, getFirstNonEmptyLine } from './util'
1
+ import { parsePairwiseBlocks } from './pairwise.ts'
2
+ import { parseBlocks, parseHeader, getFirstNonEmptyLine } from './util.ts'
3
3
 
4
4
  export function parseClustalIter(arr: Iterator<string>) {
5
5
  const line = getFirstNonEmptyLine(arr)
package/src/pairwise.ts CHANGED
@@ -1,40 +1,54 @@
1
- import { getFirstNonEmptyLine } from './util'
2
-
3
- export function getSeqBounds(line: string) {
4
- const fields = line.split(/\s+/)
5
- const k1 = fields[0].length + fields[1].length
6
- const temp = line.slice(k1)
7
- const s = k1 + temp.indexOf(fields[2])
8
- const e = s + fields[2].length
9
- return [s, e] as const
1
+ import { getFirstNonEmptyLine } from './util.ts'
2
+
3
+ function isSequenceLine(line: string) {
4
+ const trimmed = line.trim()
5
+ return /^\w+\s+/.test(trimmed)
6
+ }
7
+
8
+ function hasPositionNumbers(fields: string[]) {
9
+ return fields.length >= 3 && /^\d+$/.test(fields[1])
10
+ }
11
+
12
+ export function getSeqBounds(line: string, seqIndex: number) {
13
+ const trimmed = line.trim()
14
+ const fields = trimmed.split(/\s+/)
15
+ const seq = fields[seqIndex]
16
+ const seqStart = line.indexOf(seq, line.indexOf(fields[0]) + fields[0].length)
17
+ return [seqStart, seqStart + seq.length] as const
10
18
  }
11
19
 
12
20
  // Use the first block to get the sequence identifiers
13
21
  export function parsePairwiseBlock(arr: Iterator<string>) {
14
22
  let line = getFirstNonEmptyLine(arr)
15
- const block = []
23
+ const block: string[] = []
16
24
  let consensusLine = ''
17
25
  if (!line) {
18
26
  return undefined
19
27
  }
20
28
 
21
29
  while (line) {
22
- if (line.startsWith(' ')) {
23
- consensusLine = line
24
- } else {
30
+ if (isSequenceLine(line)) {
25
31
  block.push(line)
32
+ } else {
33
+ consensusLine = line
26
34
  }
27
35
  line = arr.next().value
28
36
  }
29
- const [start, end] = getSeqBounds(block[0])
30
- const fields = block.map(s => s.split(/\s+/))
37
+
38
+ if (block.length === 0) {
39
+ return undefined
40
+ }
41
+
42
+ const fields = block.map(s => s.trim().split(/\s+/))
43
+ const seqIndex = hasPositionNumbers(fields[0]) ? 2 : 1
44
+ const [start, end] = getSeqBounds(block[0], seqIndex)
31
45
  const ids = fields.map(s => s[0])
32
- const seqs = fields.map(s => s[2])
46
+ const seqs = fields.map(s => s[seqIndex])
33
47
  let consensus = consensusLine.slice(start, end)
34
48
 
35
49
  // handle if the consensus trailing whitespace got trimmed
36
50
  const remainder = seqs[0].length - consensus.length
37
- if (remainder) {
51
+ if (remainder > 0) {
38
52
  consensus += ' '.repeat(remainder)
39
53
  }
40
54
  return { ids, seqs, consensus }