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<li class="navelem"><a class="el" href="namespacebtllib.html">btllib</a></li><li class="navelem"><a class="el" href="classbtllib_1_1seedAAHash.html">seedAAHash</a></li> </ul>
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<div class="header">
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<a href="#pub-methods">Public Member Functions</a> |
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<div class="headertitle"><div class="title">btllib::seedAAHash Class Reference</div></div>
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<table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="pub-methods" name="pub-methods"></a>
Public Member Functions</h2></td></tr>
<tr class="memitem:abd41384c955f63b4145d32e8424b12ba"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classbtllib_1_1seedAAHash.html#abd41384c955f63b4145d32e8424b12ba">seedAAHash</a> (const char *seq, const std::vector< SpacedSeed > &seeds, unsigned hash_num_per_seed, unsigned k, size_t pos=0)</td></tr>
<tr class="separator:abd41384c955f63b4145d32e8424b12ba"><td class="memSeparator" colspan="2"> </td></tr>
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 </td><td class="memItemRight" valign="bottom"><b>seedAAHash</b> (const std::string &seq, const std::vector< SpacedSeed > &seeds, unsigned hash_num_per_seed, unsigned k, size_t pos=0)</td></tr>
<tr class="separator:a5a700ae9dd4d277dfb710f47909d9f26"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:af94dde6f73006fa4fae31f0a14fcac4f"><td class="memItemLeft" align="right" valign="top"><a id="af94dde6f73006fa4fae31f0a14fcac4f" name="af94dde6f73006fa4fae31f0a14fcac4f"></a>
 </td><td class="memItemRight" valign="bottom"><b>seedAAHash</b> (const char *seq, const std::vector< std::string > &seeds, unsigned hash_num_per_seed, unsigned k, size_t pos=0)</td></tr>
<tr class="separator:af94dde6f73006fa4fae31f0a14fcac4f"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aeb732b12e1f6ad348aa89c83d76c37fa"><td class="memItemLeft" align="right" valign="top"><a id="aeb732b12e1f6ad348aa89c83d76c37fa" name="aeb732b12e1f6ad348aa89c83d76c37fa"></a>
 </td><td class="memItemRight" valign="bottom"><b>seedAAHash</b> (const std::string &seq, const std::vector< std::string > &seeds, unsigned hash_num_per_seed, unsigned k, size_t pos=0)</td></tr>
<tr class="separator:aeb732b12e1f6ad348aa89c83d76c37fa"><td class="memSeparator" colspan="2"> </td></tr>
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 </td><td class="memItemRight" valign="bottom"><b>seedAAHash</b> (const <a class="el" href="classbtllib_1_1seedAAHash.html">seedAAHash</a> &seed_aahash)</td></tr>
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<tr class="memitem:aa9ac90781087d0d5104a29c1798fcff1"><td class="memItemLeft" align="right" valign="top"><a id="aa9ac90781087d0d5104a29c1798fcff1" name="aa9ac90781087d0d5104a29c1798fcff1"></a>
 </td><td class="memItemRight" valign="bottom"><b>seedAAHash</b> (<a class="el" href="classbtllib_1_1seedAAHash.html">seedAAHash</a> &&)=default</td></tr>
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<tr class="memitem:a46a083452c16d8d2bb95ae9ccaca83e6"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classbtllib_1_1seedAAHash.html#a46a083452c16d8d2bb95ae9ccaca83e6">roll</a> ()</td></tr>
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const uint64_t * </td><td class="memItemRight" valign="bottom"><b>hashes</b> () const</td></tr>
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size_t </td><td class="memItemRight" valign="bottom"><b>get_pos</b> () const</td></tr>
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unsigned </td><td class="memItemRight" valign="bottom"><b>get_hash_num</b> () const</td></tr>
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unsigned </td><td class="memItemRight" valign="bottom"><b>get_hash_num_per_seed</b> () const</td></tr>
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unsigned </td><td class="memItemRight" valign="bottom"><b>get_k</b> () const</td></tr>
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<h2 class="groupheader">Constructor & Destructor Documentation</h2>
<a id="abd41384c955f63b4145d32e8424b12ba" name="abd41384c955f63b4145d32e8424b12ba"></a>
<h2 class="memtitle"><span class="permalink"><a href="#abd41384c955f63b4145d32e8424b12ba">◆ </a></span>seedAAHash()</h2>
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<td class="memname">btllib::seedAAHash::seedAAHash </td>
<td>(</td>
<td class="paramtype">const char * </td>
<td class="paramname"><em>seq</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">const std::vector< SpacedSeed > & </td>
<td class="paramname"><em>seeds</em>, </td>
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<td class="paramkey"></td>
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<td class="paramtype">unsigned </td>
<td class="paramname"><em>hash_num_per_seed</em>, </td>
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<td class="paramtype">unsigned </td>
<td class="paramname"><em>k</em>, </td>
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<td class="paramkey"></td>
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<td class="paramtype">size_t </td>
<td class="paramname"><em>pos</em> = <code>0</code> </td>
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<td>)</td>
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<p>Constructor. </p><dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">seq</td><td>String of DNA sequence to be hashed. </td></tr>
<tr><td class="paramname">seeds</td><td>Multi-level seeds to use for hashing. </td></tr>
<tr><td class="paramname">hash_num_per_seed</td><td>Number of hashes to produce per seed. </td></tr>
<tr><td class="paramname">k</td><td>K-mer size. </td></tr>
<tr><td class="paramname">pos</td><td>Position in seq to start hashing from. </td></tr>
</table>
</dd>
</dl>
</div>
</div>
<h2 class="groupheader">Member Function Documentation</h2>
<a id="a46a083452c16d8d2bb95ae9ccaca83e6" name="a46a083452c16d8d2bb95ae9ccaca83e6"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a46a083452c16d8d2bb95ae9ccaca83e6">◆ </a></span>roll()</h2>
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<td class="memname">bool btllib::seedAAHash::roll </td>
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<p>Calculate the hash values of current k-mer based on the seed(s) and advance to the next. <a class="el" href="classbtllib_1_1seedAAHash.html">seedAAHash</a> advances one amino acid at a time until it finds a k-mer with valid characters and skips over those with invalid characters. This method must be called before hashes() is accessed, for the first and every subsequent hashed kmer. get_pos() may be called at any time to obtain the position of last hashed k-mer or the k-mer to be hashed if <a class="el" href="classbtllib_1_1seedAAHash.html#a46a083452c16d8d2bb95ae9ccaca83e6">roll()</a> has never been called on this <a class="el" href="classbtllib_1_1AAHash.html">AAHash</a> object. It is important to note that the number of <a class="el" href="classbtllib_1_1seedAAHash.html#a46a083452c16d8d2bb95ae9ccaca83e6">roll()</a> calls is NOT necessarily equal to get_pos(), if there are N or invalid characters in the hashed sequence.</p>
<dl class="section return"><dt>Returns</dt><dd>true on success and false otherwise. </dd></dl>
</div>
</div>
<hr/>The documentation for this class was generated from the following file:<ul>
<li>include/btllib/<a class="el" href="aahash_8hpp_source.html">aahash.hpp</a></li>
</ul>
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