-
Notifications
You must be signed in to change notification settings - Fork 6
/
Copy pathclassbtllib_1_1AAHash.html
224 lines (218 loc) · 13.5 KB
/
classbtllib_1_1AAHash.html
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "https://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en-US">
<head>
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
<meta http-equiv="X-UA-Compatible" content="IE=11"/>
<meta name="generator" content="Doxygen 1.11.0"/>
<meta name="viewport" content="width=device-width, initial-scale=1"/>
<title>btllib: btllib::AAHash Class Reference</title>
<link href="tabs.css" rel="stylesheet" type="text/css"/>
<script type="text/javascript" src="jquery.js"></script>
<script type="text/javascript" src="dynsections.js"></script>
<script type="text/javascript" src="clipboard.js"></script>
<link href="navtree.css" rel="stylesheet" type="text/css"/>
<script type="text/javascript" src="resize.js"></script>
<script type="text/javascript" src="cookie.js"></script>
<link href="search/search.css" rel="stylesheet" type="text/css"/>
<script type="text/javascript" src="search/searchdata.js"></script>
<script type="text/javascript" src="search/search.js"></script>
<link href="doxygen.css" rel="stylesheet" type="text/css" />
</head>
<body>
<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
<div id="titlearea">
<table cellspacing="0" cellpadding="0">
<tbody>
<tr id="projectrow">
<td id="projectalign">
<div id="projectname">btllib
</div>
</td>
</tr>
</tbody>
</table>
</div>
<!-- end header part -->
<!-- Generated by Doxygen 1.11.0 -->
<script type="text/javascript">
/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&dn=expat.txt MIT */
var searchBox = new SearchBox("searchBox", "search/",'.html');
/* @license-end */
</script>
<script type="text/javascript">
/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&dn=expat.txt MIT */
$(function() { codefold.init(0); });
/* @license-end */
</script>
<script type="text/javascript" src="menudata.js"></script>
<script type="text/javascript" src="menu.js"></script>
<script type="text/javascript">
/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&dn=expat.txt MIT */
$(function() {
initMenu('',true,false,'search.php','Search',false);
$(function() { init_search(); });
});
/* @license-end */
</script>
<div id="main-nav"></div>
<script type="text/javascript">
/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&dn=expat.txt MIT */
$(function(){ initResizable(false); });
/* @license-end */
</script>
<!-- window showing the filter options -->
<div id="MSearchSelectWindow"
onmouseover="return searchBox.OnSearchSelectShow()"
onmouseout="return searchBox.OnSearchSelectHide()"
onkeydown="return searchBox.OnSearchSelectKey(event)">
</div>
<!-- iframe showing the search results (closed by default) -->
<div id="MSearchResultsWindow">
<div id="MSearchResults">
<div class="SRPage">
<div id="SRIndex">
<div id="SRResults"></div>
<div class="SRStatus" id="Loading">Loading...</div>
<div class="SRStatus" id="Searching">Searching...</div>
<div class="SRStatus" id="NoMatches">No Matches</div>
</div>
</div>
</div>
</div>
<div id="nav-path" class="navpath">
<ul>
<li class="navelem"><a class="el" href="namespacebtllib.html">btllib</a></li><li class="navelem"><a class="el" href="classbtllib_1_1AAHash.html">AAHash</a></li> </ul>
</div>
</div><!-- top -->
<div id="doc-content">
<div class="header">
<div class="summary">
<a href="#pub-methods">Public Member Functions</a> |
<a href="#friends">Friends</a> |
<a href="classbtllib_1_1AAHash-members.html">List of all members</a> </div>
<div class="headertitle"><div class="title">btllib::AAHash Class Reference</div></div>
</div><!--header-->
<div class="contents">
<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:a2edba2dba416e5913a9867fec2fd5444" id="r_a2edba2dba416e5913a9867fec2fd5444"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="#a2edba2dba416e5913a9867fec2fd5444">AAHash</a> (std::string_view seq, uint8_t hash_num, uint16_t k, unsigned level, size_t pos=0)</td></tr>
<tr class="separator:a2edba2dba416e5913a9867fec2fd5444"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ac0f4e49197cf9822a1d44795fe992de9" id="r_ac0f4e49197cf9822a1d44795fe992de9"><td class="memItemLeft" align="right" valign="top"><a id="ac0f4e49197cf9822a1d44795fe992de9" name="ac0f4e49197cf9822a1d44795fe992de9"></a>
 </td><td class="memItemRight" valign="bottom"><b>AAHash</b> (const <a class="el" href="classbtllib_1_1AAHash.html">AAHash</a> &aahash)</td></tr>
<tr class="separator:ac0f4e49197cf9822a1d44795fe992de9"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a82e59cc84a2afe87fbde0052a579510d" id="r_a82e59cc84a2afe87fbde0052a579510d"><td class="memItemLeft" align="right" valign="top"><a id="a82e59cc84a2afe87fbde0052a579510d" name="a82e59cc84a2afe87fbde0052a579510d"></a>
 </td><td class="memItemRight" valign="bottom"><b>AAHash</b> (<a class="el" href="classbtllib_1_1AAHash.html">AAHash</a> &&)=default</td></tr>
<tr class="separator:a82e59cc84a2afe87fbde0052a579510d"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a94a48eac3e812204810c3182f55b122f" id="r_a94a48eac3e812204810c3182f55b122f"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="#a94a48eac3e812204810c3182f55b122f">roll</a> ()</td></tr>
<tr class="separator:a94a48eac3e812204810c3182f55b122f"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a3b4543e290ae60fe81183fabfbf8f047" id="r_a3b4543e290ae60fe81183fabfbf8f047"><td class="memItemLeft" align="right" valign="top"><a id="a3b4543e290ae60fe81183fabfbf8f047" name="a3b4543e290ae60fe81183fabfbf8f047"></a>
const uint64_t * </td><td class="memItemRight" valign="bottom"><b>hashes</b> () const</td></tr>
<tr class="separator:a3b4543e290ae60fe81183fabfbf8f047"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a6f78f4e59c0e9ab54dcc6e0b3f3aa9fb" id="r_a6f78f4e59c0e9ab54dcc6e0b3f3aa9fb"><td class="memItemLeft" align="right" valign="top"><a id="a6f78f4e59c0e9ab54dcc6e0b3f3aa9fb" name="a6f78f4e59c0e9ab54dcc6e0b3f3aa9fb"></a>
size_t </td><td class="memItemRight" valign="bottom"><b>get_pos</b> () const</td></tr>
<tr class="separator:a6f78f4e59c0e9ab54dcc6e0b3f3aa9fb"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aff3cebbe15c1be78aec8ba7c7ad42819" id="r_aff3cebbe15c1be78aec8ba7c7ad42819"><td class="memItemLeft" align="right" valign="top"><a id="aff3cebbe15c1be78aec8ba7c7ad42819" name="aff3cebbe15c1be78aec8ba7c7ad42819"></a>
unsigned </td><td class="memItemRight" valign="bottom"><b>get_hash_num</b> () const</td></tr>
<tr class="separator:aff3cebbe15c1be78aec8ba7c7ad42819"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a79222ca85fac4f99ea9ca1fc082a4c60" id="r_a79222ca85fac4f99ea9ca1fc082a4c60"><td class="memItemLeft" align="right" valign="top"><a id="a79222ca85fac4f99ea9ca1fc082a4c60" name="a79222ca85fac4f99ea9ca1fc082a4c60"></a>
unsigned </td><td class="memItemRight" valign="bottom"><b>get_k</b> () const</td></tr>
<tr class="separator:a79222ca85fac4f99ea9ca1fc082a4c60"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a9a5b61f74c111a639751a444f8a595a8" id="r_a9a5b61f74c111a639751a444f8a595a8"><td class="memItemLeft" align="right" valign="top"><a id="a9a5b61f74c111a639751a444f8a595a8" name="a9a5b61f74c111a639751a444f8a595a8"></a>
uint64_t </td><td class="memItemRight" valign="bottom"><b>get_forward_hash</b> () const</td></tr>
<tr class="separator:a9a5b61f74c111a639751a444f8a595a8"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ab79fb4abfe4eb1acf6706e3611648827" id="r_ab79fb4abfe4eb1acf6706e3611648827"><td class="memItemLeft" align="right" valign="top"><a id="ab79fb4abfe4eb1acf6706e3611648827" name="ab79fb4abfe4eb1acf6706e3611648827"></a>
unsigned </td><td class="memItemRight" valign="bottom"><b>get_level</b> () const</td></tr>
<tr class="separator:ab79fb4abfe4eb1acf6706e3611648827"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:afd28256546e0bf1e1ac6fd34cd580ff7" id="r_afd28256546e0bf1e1ac6fd34cd580ff7"><td class="memItemLeft" align="right" valign="top"><a id="afd28256546e0bf1e1ac6fd34cd580ff7" name="afd28256546e0bf1e1ac6fd34cd580ff7"></a>
const char * </td><td class="memItemRight" valign="bottom"><b>get_seq</b> () const</td></tr>
<tr class="separator:afd28256546e0bf1e1ac6fd34cd580ff7"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="friends" name="friends"></a>
Friends</h2></td></tr>
<tr class="memitem:a60676b3e75c863f4a3276e15cc5a5583" id="r_a60676b3e75c863f4a3276e15cc5a5583"><td class="memItemLeft" align="right" valign="top"><a id="a60676b3e75c863f4a3276e15cc5a5583" name="a60676b3e75c863f4a3276e15cc5a5583"></a>
class </td><td class="memItemRight" valign="bottom"><b>SeedAAHash</b></td></tr>
<tr class="separator:a60676b3e75c863f4a3276e15cc5a5583"><td class="memSeparator" colspan="2"> </td></tr>
</table>
<h2 class="groupheader">Constructor & Destructor Documentation</h2>
<a id="a2edba2dba416e5913a9867fec2fd5444" name="a2edba2dba416e5913a9867fec2fd5444"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a2edba2dba416e5913a9867fec2fd5444">◆ </a></span>AAHash()</h2>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">btllib::AAHash::AAHash </td>
<td>(</td>
<td class="paramtype">std::string_view</td> <td class="paramname"><span class="paramname"><em>seq</em></span>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">uint8_t</td> <td class="paramname"><span class="paramname"><em>hash_num</em></span>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">uint16_t</td> <td class="paramname"><span class="paramname"><em>k</em></span>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">unsigned</td> <td class="paramname"><span class="paramname"><em>level</em></span>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">size_t</td> <td class="paramname"><span class="paramname"><em>pos</em></span><span class="paramdefsep"> = </span><span class="paramdefval">0</span> )</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>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">hash_num</td><td>Number of hashes to produce per k-mer. </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>
<tr><td class="paramname">level</td><td>seed level to generate hash. </td></tr>
</table>
</dd>
</dl>
</div>
</div>
<h2 class="groupheader">Member Function Documentation</h2>
<a id="a94a48eac3e812204810c3182f55b122f" name="a94a48eac3e812204810c3182f55b122f"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a94a48eac3e812204810c3182f55b122f">◆ </a></span>roll()</h2>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">bool btllib::AAHash::roll </td>
<td>(</td>
<td class="paramname"><span class="paramname"><em></em></span></td><td>)</td>
<td></td>
</tr>
</table>
</div><div class="memdoc">
<p>Calculate the hash values of current k-mer and advance to the next. <a class="el" href="classbtllib_1_1AAHash.html">AAHash</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="#a94a48eac3e812204810c3182f55b122f">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="#a94a48eac3e812204810c3182f55b122f">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>
</div><!-- contents -->
<!-- start footer part -->
<hr class="footer"/><address class="footer"><small>
Generated by <a href="https://www.doxygen.org/index.html"><img class="footer" src="doxygen.svg" width="104" height="31" alt="doxygen"/></a> 1.11.0
</small></address>
</div><!-- doc-content -->
</body>
</html>