Add a setter method for seq in ntHash

docs/classbtllib_1_1NtHash-members.html

@@ -109,7 +109,8 @@
   <tr><td class="entry"><a class="el" href="classbtllib_1_1NtHash.html#a8c17ba730f3539ab9673186cd556d742">peek_back</a>(char char_in)</td><td class="entry"><a class="el" href="classbtllib_1_1NtHash.html">btllib::NtHash</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
   <tr class="even"><td class="entry"><a class="el" href="classbtllib_1_1NtHash.html#a244c0c11655b6e1c52dd7c4528b8ed05">roll</a>()</td><td class="entry"><a class="el" href="classbtllib_1_1NtHash.html">btllib::NtHash</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
   <tr><td class="entry"><a class="el" href="classbtllib_1_1NtHash.html#ae4417f1829a2eaa3a19559ee68df1091">roll_back</a>()</td><td class="entry"><a class="el" href="classbtllib_1_1NtHash.html">btllib::NtHash</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
-  <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>sub</b>(const std::vector&lt; unsigned &gt; &amp;positions, const std::vector&lt; unsigned char &gt; &amp;new_bases) (defined in <a class="el" href="classbtllib_1_1NtHash.html">btllib::NtHash</a>)</td><td class="entry"><a class="el" href="classbtllib_1_1NtHash.html">btllib::NtHash</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classbtllib_1_1NtHash.html#a419ba8aaab69033241dece2511082ad7">set_seq</a>(const std::string &amp;seq, size_t pos=0)</td><td class="entry"><a class="el" href="classbtllib_1_1NtHash.html">btllib::NtHash</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
+  <tr bgcolor="#f0f0f0"><td class="entry"><b>sub</b>(const std::vector&lt; unsigned &gt; &amp;positions, const std::vector&lt; unsigned char &gt; &amp;new_bases) (defined in <a class="el" href="classbtllib_1_1NtHash.html">btllib::NtHash</a>)</td><td class="entry"><a class="el" href="classbtllib_1_1NtHash.html">btllib::NtHash</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
 </table></div><!-- contents -->
 <!-- start footer part -->
 <hr class="footer"/><address class="footer"><small>

docs/classbtllib_1_1NtHash.html

@@ -108,6 +108,8 @@
 <tr class="memitem:a02580f5bf9c028283228e8148ffc10e5"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a02580f5bf9c028283228e8148ffc10e5"></a>
 &#160;</td><td class="memItemRight" valign="bottom"><b>NtHash</b> (<a class="el" href="classbtllib_1_1NtHash.html">NtHash</a> &amp;&amp;)=default</td></tr>
 <tr class="separator:a02580f5bf9c028283228e8148ffc10e5"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a419ba8aaab69033241dece2511082ad7"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classbtllib_1_1NtHash.html#a419ba8aaab69033241dece2511082ad7">set_seq</a> (const std::string &amp;seq, size_t pos=0)</td></tr>
+<tr class="separator:a419ba8aaab69033241dece2511082ad7"><td class="memSeparator" colspan="2">&#160;</td></tr>
 <tr class="memitem:a244c0c11655b6e1c52dd7c4528b8ed05"><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classbtllib_1_1NtHash.html#a244c0c11655b6e1c52dd7c4528b8ed05">roll</a> ()</td></tr>
 <tr class="separator:a244c0c11655b6e1c52dd7c4528b8ed05"><td class="memSeparator" colspan="2">&#160;</td></tr>
 <tr class="memitem:ae4417f1829a2eaa3a19559ee68df1091"><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classbtllib_1_1NtHash.html#ae4417f1829a2eaa3a19559ee68df1091">roll_back</a> ()</td></tr>
@@ -559,6 +561,47 @@ <h2 class="groupheader">Member Function Documentation</h2>
 <p>Like the <a class="el" href="classbtllib_1_1NtHash.html#a244c0c11655b6e1c52dd7c4528b8ed05">roll()</a> function, but advance backwards. </p>
 <dl class="section return"><dt>Returns</dt><dd><code>true</code> on success and <code>false</code> otherwise </dd></dl>
 
+</div>
+</div>
+<a class="anchor" id="a419ba8aaab69033241dece2511082ad7"></a>
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">void btllib::NtHash::set_seq </td>
+          <td>(</td>
+          <td class="paramtype">const std::string &amp;&#160;</td>
+          <td class="paramname"><em>seq</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">size_t&#160;</td>
+          <td class="paramname"><em>pos</em> = <code>0</code>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel">inline</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+<p>Reset iterator on a new sequence. Useful for re-using <a class="el" href="classbtllib_1_1NtHash.html">NtHash</a> objects. </p>
+<dl class="params"><dt>Parameters</dt><dd>
+  <table class="params">
+    <tr><td class="paramname">seq</td><td>New sequence for hashing </td></tr>
+  </table>
+  </dd>
+</dl>
+
 </div>
 </div>
 <hr/>The documentation for this class was generated from the following file:<ul>

docs/classbtllib_1_1SeedNtHash-members.html

@@ -112,6 +112,7 @@
   <tr class="even"><td class="entry"><a class="el" href="classbtllib_1_1SeedNtHash.html#ac37315348fc391ab9e795e4e700fdb21">SeedNtHash</a>(const std::string &amp;seq, const std::vector&lt; std::vector&lt; unsigned &gt;&gt; &amp;seeds, hashing_internals::NUM_HASHES_TYPE num_hashes_per_seed, hashing_internals::K_TYPE k, size_t pos=0)</td><td class="entry"><a class="el" href="classbtllib_1_1SeedNtHash.html">btllib::SeedNtHash</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
   <tr bgcolor="#f0f0f0"><td class="entry"><b>SeedNtHash</b>(const SeedNtHash &amp;obj) (defined in <a class="el" href="classbtllib_1_1SeedNtHash.html">btllib::SeedNtHash</a>)</td><td class="entry"><a class="el" href="classbtllib_1_1SeedNtHash.html">btllib::SeedNtHash</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
   <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>SeedNtHash</b>(SeedNtHash &amp;&amp;)=default (defined in <a class="el" href="classbtllib_1_1SeedNtHash.html">btllib::SeedNtHash</a>)</td><td class="entry"><a class="el" href="classbtllib_1_1SeedNtHash.html">btllib::SeedNtHash</a></td><td class="entry"></td></tr>
+  <tr><td class="entry"><a class="el" href="classbtllib_1_1SeedNtHash.html#a49ff99a34ead2b1571a05806607746d0">set_seq</a>(const std::string &amp;seq, size_t pos=0)</td><td class="entry"><a class="el" href="classbtllib_1_1SeedNtHash.html">btllib::SeedNtHash</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
 </table></div><!-- contents -->
 <!-- start footer part -->
 <hr class="footer"/><address class="footer"><small>

docs/classbtllib_1_1SeedNtHash.html

@@ -112,6 +112,8 @@
 <tr class="memitem:aef7d081543cac6f9357b17a05214a0f5"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="aef7d081543cac6f9357b17a05214a0f5"></a>
 &#160;</td><td class="memItemRight" valign="bottom"><b>SeedNtHash</b> (<a class="el" href="classbtllib_1_1SeedNtHash.html">SeedNtHash</a> &amp;&amp;)=default</td></tr>
 <tr class="separator:aef7d081543cac6f9357b17a05214a0f5"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a49ff99a34ead2b1571a05806607746d0"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classbtllib_1_1SeedNtHash.html#a49ff99a34ead2b1571a05806607746d0">set_seq</a> (const std::string &amp;seq, size_t pos=0)</td></tr>
+<tr class="separator:a49ff99a34ead2b1571a05806607746d0"><td class="memSeparator" colspan="2">&#160;</td></tr>
 <tr class="memitem:aa817b8acaf7c57d7be8ce47fcf5ac758"><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classbtllib_1_1SeedNtHash.html#aa817b8acaf7c57d7be8ce47fcf5ac758">roll</a> ()</td></tr>
 <tr class="separator:aa817b8acaf7c57d7be8ce47fcf5ac758"><td class="memSeparator" colspan="2">&#160;</td></tr>
 <tr class="memitem:a293e694de84eafbb19bf7123749f9ba6"><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classbtllib_1_1SeedNtHash.html#a293e694de84eafbb19bf7123749f9ba6">roll_back</a> ()</td></tr>
@@ -734,6 +736,47 @@ <h2 class="groupheader">Member Function Documentation</h2>
 <p>Like the <a class="el" href="classbtllib_1_1SeedNtHash.html#aa817b8acaf7c57d7be8ce47fcf5ac758">roll()</a> function, but advance backwards. </p>
 <dl class="section return"><dt>Returns</dt><dd><code>true</code> on success and <code>false</code> otherwise. </dd></dl>
 
+</div>
+</div>
+<a class="anchor" id="a49ff99a34ead2b1571a05806607746d0"></a>
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">void btllib::SeedNtHash::set_seq </td>
+          <td>(</td>
+          <td class="paramtype">const std::string &amp;&#160;</td>
+          <td class="paramname"><em>seq</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">size_t&#160;</td>
+          <td class="paramname"><em>pos</em> = <code>0</code>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel">inline</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+<p>Reset iterator on a new sequence. Useful for re-using <a class="el" href="classbtllib_1_1NtHash.html">NtHash</a> objects. </p>
+<dl class="params"><dt>Parameters</dt><dd>
+  <table class="params">
+    <tr><td class="paramname">seq</td><td>New sequence for hashing </td></tr>
+  </table>
+  </dd>
+</dl>
+
 </div>
 </div>
 <hr/>The documentation for this class was generated from the following file:<ul>

docs/counting__bloom__filter-inl_8hpp_source.html

@@ -517,7 +517,7 @@
 <div class="ttc" id="classbtllib_1_1CountingBloomFilter_html"><div class="ttname"><a href="classbtllib_1_1CountingBloomFilter.html">btllib::CountingBloomFilter</a></div><div class="ttdef"><b>Definition:</b> counting_bloom_filter.hpp:42</div></div>
 <div class="ttc" id="namespacebtllib_html_a60a36f4583a7eb03001f8bdb7b395507"><div class="ttname"><a href="namespacebtllib.html#a60a36f4583a7eb03001f8bdb7b395507">btllib::check_warning</a></div><div class="ttdeci">void check_warning(bool condition, const std::string &amp;msg)</div></div>
 <div class="ttc" id="classbtllib_1_1KmerCountingBloomFilter_html_a1593f904f0bd79534b1527ae20fe375f"><div class="ttname"><a href="classbtllib_1_1KmerCountingBloomFilter.html#a1593f904f0bd79534b1527ae20fe375f">btllib::KmerCountingBloomFilter::clear</a></div><div class="ttdeci">void clear(const char *seq, size_t seq_len)</div><div class="ttdef"><b>Definition:</b> counting_bloom_filter-inl.hpp:289</div></div>
-<div class="ttc" id="classbtllib_1_1NtHash_html_ad3b51e8a4a12d4136783fc40fb5b0439"><div class="ttname"><a href="classbtllib_1_1NtHash.html#ad3b51e8a4a12d4136783fc40fb5b0439">btllib::NtHash::hashes</a></div><div class="ttdeci">const uint64_t * hashes() const </div><div class="ttdef"><b>Definition:</b> nthash_kmer.hpp:443</div></div>
+<div class="ttc" id="classbtllib_1_1NtHash_html_ad3b51e8a4a12d4136783fc40fb5b0439"><div class="ttname"><a href="classbtllib_1_1NtHash.html#ad3b51e8a4a12d4136783fc40fb5b0439">btllib::NtHash::hashes</a></div><div class="ttdeci">const uint64_t * hashes() const </div><div class="ttdef"><b>Definition:</b> nthash_kmer.hpp:463</div></div>
 <div class="ttc" id="classbtllib_1_1CountingBloomFilter_html_a1d73900df10374cbc08a8eb5f8e0ffa3"><div class="ttname"><a href="classbtllib_1_1CountingBloomFilter.html#a1d73900df10374cbc08a8eb5f8e0ffa3">btllib::CountingBloomFilter::remove</a></div><div class="ttdeci">void remove(const uint64_t *hashes)</div><div class="ttdef"><b>Definition:</b> counting_bloom_filter-inl.hpp:89</div></div>
 <div class="ttc" id="classbtllib_1_1KmerCountingBloomFilter_html_a69331bd22706ca7676a1ca08867f42e2"><div class="ttname"><a href="classbtllib_1_1KmerCountingBloomFilter.html#a69331bd22706ca7676a1ca08867f42e2">btllib::KmerCountingBloomFilter::contains_insert_thresh</a></div><div class="ttdeci">T contains_insert_thresh(const char *seq, size_t seq_len, T threshold)</div><div class="ttdef"><b>Definition:</b> counting_bloom_filter-inl.hpp:350</div></div>
 <div class="ttc" id="classbtllib_1_1NtHash_html"><div class="ttname"><a href="classbtllib_1_1NtHash.html">btllib::NtHash</a></div><div class="ttdef"><b>Definition:</b> nthash_kmer.hpp:236</div></div>
@@ -531,7 +531,7 @@
 <div class="ttc" id="classbtllib_1_1CountingBloomFilter_html_a2aa206e822285afce3c5a8f0ab02c679"><div class="ttname"><a href="classbtllib_1_1CountingBloomFilter.html#a2aa206e822285afce3c5a8f0ab02c679">btllib::CountingBloomFilter::get_pop_cnt</a></div><div class="ttdeci">uint64_t get_pop_cnt(T threshold=1) const </div><div class="ttdef"><b>Definition:</b> counting_bloom_filter-inl.hpp:167</div></div>
 <div class="ttc" id="classbtllib_1_1KmerCountingBloomFilter_html_aab2f78777fa04950abd2197bd12bf6cb"><div class="ttname"><a href="classbtllib_1_1KmerCountingBloomFilter.html#aab2f78777fa04950abd2197bd12bf6cb">btllib::KmerCountingBloomFilter::contains_insert</a></div><div class="ttdeci">T contains_insert(const char *seq, size_t seq_len)</div><div class="ttdef"><b>Definition:</b> counting_bloom_filter-inl.hpp:311</div></div>
 <div class="ttc" id="classbtllib_1_1CountingBloomFilter_html_afbb0e0975acd76ec46377d8c58570419"><div class="ttname"><a href="classbtllib_1_1CountingBloomFilter.html#afbb0e0975acd76ec46377d8c58570419">btllib::CountingBloomFilter::get_occupancy</a></div><div class="ttdeci">double get_occupancy(T threshold=1) const </div><div class="ttdef"><b>Definition:</b> counting_bloom_filter-inl.hpp:184</div></div>
-<div class="ttc" id="classbtllib_1_1NtHash_html_a244c0c11655b6e1c52dd7c4528b8ed05"><div class="ttname"><a href="classbtllib_1_1NtHash.html#a244c0c11655b6e1c52dd7c4528b8ed05">btllib::NtHash::roll</a></div><div class="ttdeci">bool roll()</div><div class="ttdef"><b>Definition:</b> nthash_kmer.hpp:315</div></div>
+<div class="ttc" id="classbtllib_1_1NtHash_html_a244c0c11655b6e1c52dd7c4528b8ed05"><div class="ttname"><a href="classbtllib_1_1NtHash.html#a244c0c11655b6e1c52dd7c4528b8ed05">btllib::NtHash::roll</a></div><div class="ttdeci">bool roll()</div><div class="ttdef"><b>Definition:</b> nthash_kmer.hpp:335</div></div>
 <div class="ttc" id="classbtllib_1_1KmerCountingBloomFilter_html_a3dbe61dad343cd8a15b16817fe039fca"><div class="ttname"><a href="classbtllib_1_1KmerCountingBloomFilter.html#a3dbe61dad343cd8a15b16817fe039fca">btllib::KmerCountingBloomFilter::insert_thresh_contains</a></div><div class="ttdeci">T insert_thresh_contains(const char *seq, size_t seq_len, T threshold)</div><div class="ttdef"><b>Definition:</b> counting_bloom_filter-inl.hpp:335</div></div>
 <div class="ttc" id="classbtllib_1_1CountingBloomFilter_html_ac2929baf21cc2a2e6050af7ff314bac2"><div class="ttname"><a href="classbtllib_1_1CountingBloomFilter.html#ac2929baf21cc2a2e6050af7ff314bac2">btllib::CountingBloomFilter::insert_contains</a></div><div class="ttdeci">T insert_contains(const uint64_t *hashes, T n=1)</div><div class="ttdef"><b>Definition:</b> counting_bloom_filter-inl.hpp:130</div></div>
 <div class="ttc" id="classbtllib_1_1KmerCountingBloomFilter_html_a9f5ab29059b0fa1cc5b076520639f14c"><div class="ttname"><a href="classbtllib_1_1KmerCountingBloomFilter.html#a9f5ab29059b0fa1cc5b076520639f14c">btllib::KmerCountingBloomFilter::insert</a></div><div class="ttdeci">void insert(const char *seq, size_t seq_len)</div><div class="ttdef"><b>Definition:</b> counting_bloom_filter-inl.hpp:269</div></div>

docs/functions_0x73.html

@@ -126,7 +126,7 @@ <h3><a class="anchor" id="index_s"></a>- s -</h3><ul>
 : <a class="el" href="classbtllib_1_1SeedBloomFilter.html#a4fb38186f959cd49479404dd9e03c596">btllib::SeedBloomFilter</a>
 </li>
 <li>SeedNtHash()
-: <a class="el" href="classbtllib_1_1SeedNtHash.html#a650de4cf7e6ed95ee9dead6e23171d44">btllib::SeedNtHash</a>
+: <a class="el" href="classbtllib_1_1SeedNtHash.html#adc6e950dac4dbdd41190f1e1159c27a8">btllib::SeedNtHash</a>
 </li>
 <li>SEQ
 : <a class="el" href="structbtllib_1_1Indexlr_1_1Flag.html#a1071f9e151bc7b70631263f8e3eea180">btllib::Indexlr::Flag</a>
@@ -140,6 +140,10 @@ <h3><a class="anchor" id="index_s"></a>- s -</h3><ul>
 <li>set_seed()
 : <a class="el" href="classbtllib_1_1RandSeq.html#a0a481fe231a3ca8021aa807f2bd7d97b">btllib::RandSeq</a>
 </li>
+<li>set_seq()
+: <a class="el" href="classbtllib_1_1NtHash.html#a419ba8aaab69033241dece2511082ad7">btllib::NtHash</a>
+, <a class="el" href="classbtllib_1_1SeedNtHash.html#a49ff99a34ead2b1571a05806607746d0">btllib::SeedNtHash</a>
+</li>
 <li>SHORT_MODE
 : <a class="el" href="structbtllib_1_1SeqReader_1_1Flag.html#ab0aba3f99ab4159205621e2242c6e18f">btllib::SeqReader::Flag</a>
 , <a class="el" href="structbtllib_1_1Indexlr_1_1Flag.html#ad901a6d96362ce4b250fa144fe9a76ef">btllib::Indexlr::Flag</a>

docs/functions_func_0x73.html

@@ -122,7 +122,7 @@ <h3><a class="anchor" id="index_s"></a>- s -</h3><ul>
 : <a class="el" href="classbtllib_1_1SeedBloomFilter.html#a4fb38186f959cd49479404dd9e03c596">btllib::SeedBloomFilter</a>
 </li>
 <li>SeedNtHash()
-: <a class="el" href="classbtllib_1_1SeedNtHash.html#a650de4cf7e6ed95ee9dead6e23171d44">btllib::SeedNtHash</a>
+: <a class="el" href="classbtllib_1_1SeedNtHash.html#ac37315348fc391ab9e795e4e700fdb21">btllib::SeedNtHash</a>
 </li>
 <li>SeqReader()
 : <a class="el" href="classbtllib_1_1SeqReader.html#a03cc4e39fffc556a2f05c30bc6d3731d">btllib::SeqReader</a>
@@ -133,6 +133,10 @@ <h3><a class="anchor" id="index_s"></a>- s -</h3><ul>
 <li>set_seed()
 : <a class="el" href="classbtllib_1_1RandSeq.html#a0a481fe231a3ca8021aa807f2bd7d97b">btllib::RandSeq</a>
 </li>
+<li>set_seq()
+: <a class="el" href="classbtllib_1_1SeedNtHash.html#a49ff99a34ead2b1571a05806607746d0">btllib::SeedNtHash</a>
+, <a class="el" href="classbtllib_1_1NtHash.html#a419ba8aaab69033241dece2511082ad7">btllib::NtHash</a>
+</li>
 </ul>
 </div><!-- contents -->
 <!-- start footer part -->