sequenceserver 2.0.0 → 2.1.0

data/public/vendor/npm/through@2.3.8/test/buffering.js

@@ -1,57 +0,0 @@
-/* */ 
-var test = require("tape");
-var through = require("../index");
-test('buffering', function(assert) {
-  var ts = through(function(data) {
-    this.queue(data);
-  }, function() {
-    this.queue(null);
-  });
-  var ended = false,
-      actual = [];
-  ts.on('data', actual.push.bind(actual));
-  ts.on('end', function() {
-    ended = true;
-  });
-  ts.write(1);
-  ts.write(2);
-  ts.write(3);
-  assert.deepEqual(actual, [1, 2, 3]);
-  ts.pause();
-  ts.write(4);
-  ts.write(5);
-  ts.write(6);
-  assert.deepEqual(actual, [1, 2, 3]);
-  ts.resume();
-  assert.deepEqual(actual, [1, 2, 3, 4, 5, 6]);
-  ts.pause();
-  ts.end();
-  assert.ok(!ended);
-  ts.resume();
-  assert.ok(ended);
-  assert.end();
-});
-test('buffering has data in queue, when ends', function(assert) {
-  var ts = through(function(data) {
-    this.queue(data);
-  }, function() {
-    this.queue(null);
-  });
-  var ended = false,
-      actual = [];
-  ts.on('data', actual.push.bind(actual));
-  ts.on('end', function() {
-    ended = true;
-  });
-  ts.pause();
-  ts.write(1);
-  ts.write(2);
-  ts.write(3);
-  ts.end();
-  assert.deepEqual(actual, [], 'no data written yet, still paused');
-  assert.ok(!ended, 'end not emitted yet, still paused');
-  ts.resume();
-  assert.deepEqual(actual, [1, 2, 3], 'resumed, all data should be delivered');
-  assert.ok(ended, 'end should be emitted once all data was delivered');
-  assert.end();
-});

data/public/vendor/npm/through@2.3.8/test/end.js

@@ -1,37 +0,0 @@
-/* */ 
-var test = require("tape");
-var through = require("../index");
-test('end before close', function(assert) {
-  var ts = through();
-  var ended = false,
-      closed = false;
-  ts.on('end', function() {
-    assert.ok(!closed);
-    ended = true;
-  });
-  ts.on('close', function() {
-    assert.ok(ended);
-    closed = true;
-  });
-  ts.write(1);
-  ts.write(2);
-  ts.write(3);
-  ts.end();
-  assert.ok(ended);
-  assert.ok(closed);
-  assert.end();
-});
-test('end only once', function(t) {
-  var ts = through();
-  var ended = false,
-      closed = false;
-  ts.on('end', function() {
-    t.equal(ended, false);
-    ended = true;
-  });
-  ts.queue(null);
-  ts.queue(null);
-  ts.queue(null);
-  ts.resume();
-  t.end();
-});

data/public/vendor/npm/through@2.3.8/test/index.js

@@ -1,98 +0,0 @@
-/* */ 
-(function(process) {
-  var test = require("tape");
-  var spec = require("stream-spec");
-  var through = require("../index");
-  function write(array, stream) {
-    array = array.slice();
-    function next() {
-      while (array.length)
-        if (stream.write(array.shift()) === false)
-          return stream.once('drain', next);
-      stream.end();
-    }
-    next();
-  }
-  function read(stream, callback) {
-    var actual = [];
-    stream.on('data', function(data) {
-      actual.push(data);
-    });
-    stream.once('end', function() {
-      callback(null, actual);
-    });
-    stream.once('error', function(err) {
-      callback(err);
-    });
-  }
-  test('simple defaults', function(assert) {
-    var l = 1000,
-        expected = [];
-    while (l--)
-      expected.push(l * Math.random());
-    var t = through();
-    var s = spec(t).through().pausable();
-    read(t, function(err, actual) {
-      assert.ifError(err);
-      assert.deepEqual(actual, expected);
-      assert.end();
-    });
-    t.on('close', s.validate);
-    write(expected, t);
-  });
-  test('simple functions', function(assert) {
-    var l = 1000,
-        expected = [];
-    while (l--)
-      expected.push(l * Math.random());
-    var t = through(function(data) {
-      this.emit('data', data * 2);
-    });
-    var s = spec(t).through().pausable();
-    read(t, function(err, actual) {
-      assert.ifError(err);
-      assert.deepEqual(actual, expected.map(function(data) {
-        return data * 2;
-      }));
-      assert.end();
-    });
-    t.on('close', s.validate);
-    write(expected, t);
-  });
-  test('pauses', function(assert) {
-    var l = 1000,
-        expected = [];
-    while (l--)
-      expected.push(l);
-    var t = through();
-    var s = spec(t).through().pausable();
-    t.on('data', function() {
-      if (Math.random() > 0.1)
-        return;
-      t.pause();
-      process.nextTick(function() {
-        t.resume();
-      });
-    });
-    read(t, function(err, actual) {
-      assert.ifError(err);
-      assert.deepEqual(actual, expected);
-    });
-    t.on('close', function() {
-      s.validate();
-      assert.end();
-    });
-    write(expected, t);
-  });
-  test('does not soft-end on `undefined`', function(assert) {
-    var stream = through(),
-        count = 0;
-    stream.on('data', function(data) {
-      count++;
-    });
-    stream.write(undefined);
-    stream.write(undefined);
-    assert.equal(count, 2);
-    assert.end();
-  });
-})(require("process"));

data/public/vendor/npm/through@2.3.8/test.js

@@ -1,2 +0,0 @@
-/* */ 
-module.exports = require('./test/index');

data/public/vendor/npm/through@2.3.8.js

@@ -1 +0,0 @@
-module.exports = require("npm:through@2.3.8/index");

data/views/_options.erb

@@ -1,156 +0,0 @@
-<%#
-
-  NOTE: The markup below is displayed in a modal window.  Use less than 70
-        characters per line to preserve formatting.
-%>
-
-<h5>General Search Options</h5>
-<ul class="list-unstyled">
-  <li>
-<pre><%= ERB::Util.h %q|-task <String>
-  Task to execute for the selected BLAST algorithm
-  Options for BLASTN:
-    'blastn'       Traditional BLASTN requiring an exact match of 11 (default)
-    'blastn-short' Optimized BLASTN for query sequences shorter than 50 nucleotides.
-    'megablast'    Traditional megablast used to find very similar sequences (e.g., intraspecies or closely related species).
-    'dc-megablast' Discontiguous megablast used to find somewhat distant sequences (e.g., interspecies).
-    'rmblastn'
-  Options for BLASTP:
-    'blastp'       Standard protein-protein comparisons (default)
-    'blastp-fast'  Faster BLASTP searches using longer words for protein seeding
-    'blastp-short' Optimized BLASTP comparisons for query sequences shorter than 30 residues
-  Options for BLASTX:
-    'blastx'       Standard nucleotide-protein comparisons (default)
-    'blastx-fast'  Optimized nucleotide-protein comparisons
-  Options for TBLASTN:
-    'tblastn'      Standard protein-nucleotide comparisons (default)
-    'tblastn-fast' Optimized protein-nucleotide comparisons
-  Not applicable for TBLASTX| %></pre>
-  </li>
-  <li>
-<pre><%= ERB::Util.h %q|-evalue <Real>
-  Expectation value (E) threshold for saving hits
-  Default = '10'| %></pre>
-  </li>
-  <li>
-<pre><%= ERB::Util.h %q|-word_size <Integer, >=2>
-  Word size for wordfinder algorithm| %></pre>
-  </li>
-  <li>
-<pre><%= ERB::Util.h %q|-gapopen <Integer>
-  Cost to open a gap| %></pre>
-  </li>
-  <li>
-<pre><%= ERB::Util.h %q|-gapextend <Integer>
-  Cost to extend a gap| %></pre>
-  </li>
-  <li>
-<pre><%= ERB::Util.h %q|-matrix <String>
-  Scoring matrix name (normally BLOSUM62)| %></pre>
-  </li>
-  <li>
-<pre><%= ERB::Util.h %q|-threshold <Real, >=0>
-  Minimum word score such that the word is added to the BLAST lookup
-  table| %></pre>
-  </li>
-  <li>
-<pre><%= ERB::Util.h %q|-comp_based_stats <String>
-  Use composition-based statistics for blastp / tblastn:
-      D or d: default (equivalent to 2)
-      0 or F or f: no composition-based statistics
-      1: Composition-based statistics as in NAR 29:2994-3005, 2001
-      2 or T or t : Composition-based score adjustment as in
-      Bioinformatics 21:902-911, 2005, conditioned on sequence
-      properties
-      3: Composition-based score adjustment as in Bioinformatics
-      21:902-911, 2005, unconditionally
-  For programs other than tblastn, must either be absent or be D, F
-  or 0
-  Default = `2'| %></pre>
-  </li>
-  <li>
-<pre><%= ERB::Util.h %q|-num_descriptions <Integer, >=0>
-  Number of database sequences to show one-line descriptions for
-  Default = `500'| %></pre>
-  </li>
-  <li>
-<pre><%= ERB::Util.h %q| -num_alignments <Integer, >=0>
-  Number of database sequences to show alignments for
-  Default = `250'| %></pre>
-  </li>
-</ul>
-
-<br/>
-
-<h5>Query filtering options</h5>
-<ul class="list-unstyled">
-  <li>
-<pre><%= ERB::Util.h %q|-seg <String>
-  Filter query sequence with SEG (Format: 'yes', 'window locut hicut',
-  or 'no' to disable)
-  Default = `no'| %></pre>
-  </li>
-  <li>
-<pre><%= ERB::Util.h %q|-soft_masking <Boolean>
-  Apply filtering locations as soft masks
-  Default = `false'| %></pre>
-  </li>
-  <li>
-<pre><%= ERB::Util.h %q|-lcase_masking
-  Use lower case filtering in query and subject sequence(s)?| %></pre>
-  </li>
-</ul>
-
-<br/>
-
-<h5>Restrict search or results</h5>
-<ul class="list-unstyled">
-  <li>
-<pre><%= ERB::Util.h %q|-gilist <String>
-  Restrict search of database to list of GI's
-    * Incompatible with:  negative_gilist, seqidlist, remote, subject,
-  subject_loc| %></pre>
-  </li>
-  <li>
-<pre><%= ERB::Util.h %q|-seqidlist <String>
-  Restrict search of database to list of SeqId's
-    * Incompatible with:  gilist, negative_gilist, remote, subject,
-  subject_loc| %></pre>
-  </li>
-  <li>
-<pre><%= ERB::Util.h %q|-negative_gilist <String>
-  Restrict search of database to everything except the listed GIs
-    * Incompatible with:  gilist, seqidlist, remote, subject,
-      subject_loc| %></pre>
-  </li>
-  <li>
-<pre><%= ERB::Util.h %q|-entrez_query <String>
-  Restrict search with the given Entrez query
-    * Requires:  remote| %></pre>
-  </li>
-  <li>
-<pre><%= ERB::Util.h %q|-db_soft_mask <String>
-  Filtering algorithm ID to apply to the BLAST database as soft masking
-    * Incompatible with:  subject, subject_loc| %></pre>
-  </li>
-  <li>
-<pre><%= ERB::Util.h %q|-culling_limit <Integer, >=0>
-  If the query range of a hit is enveloped by that of at least this
-  many higher-scoring hits, delete the hit
-    * Incompatible with:  best_hit_overhang, best_hit_score_edge| %></pre>
-  </li>
-  <li>
-<pre><%= ERB::Util.h %q|-best_hit_overhang <Real, (>0 and <0.5)>
-  Best Hit algorithm overhang value (recommended value: 0.1)
-    * Incompatible with:  culling_limit| %></pre>
-  </li>
-  <li>
-<pre><%= ERB::Util.h %q|-best_hit_score_edge <Real, (>0 and <0.5)>
-  Best Hit algorithm score edge value (recommended value: 0.1)
-    * Incompatible with:  culling_limit| %></pre>
-  </li>
-  <li>
-<pre><%= ERB::Util.h %q|-max_target_seqs <Integer, >=1>
-  Maximum number of aligned sequences to keep| %></pre>
-  </li>
-</ul>