-
Notifications
You must be signed in to change notification settings - Fork 5
/
classbtllib_1_1RollingHash.html
292 lines (283 loc) · 14.6 KB
/
classbtllib_1_1RollingHash.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
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
<!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">
<head>
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
<meta http-equiv="X-UA-Compatible" content="IE=9"/>
<meta name="generator" content="Doxygen 1.8.17"/>
<meta name="viewport" content="width=device-width, initial-scale=1"/>
<title>btllib: btllib::RollingHash 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>
<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 style="height: 56px;">
<td id="projectalign" style="padding-left: 0.5em;">
<div id="projectname">btllib
</div>
</td>
</tr>
</tbody>
</table>
</div>
<!-- end header part -->
<!-- Generated by Doxygen 1.8.17 -->
<script type="text/javascript">
/* @license magnet:?xt=urn:btih:cf05388f2679ee054f2beb29a391d25f4e673ac3&dn=gpl-2.0.txt GPL-v2 */
var searchBox = new SearchBox("searchBox", "search",false,'Search');
/* @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:cf05388f2679ee054f2beb29a391d25f4e673ac3&dn=gpl-2.0.txt GPL-v2 */
$(function() {
initMenu('',true,false,'search.php','Search');
$(document).ready(function() { init_search(); });
});
/* @license-end */</script>
<div id="main-nav"></div>
<!-- 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">
<iframe src="javascript:void(0)" frameborder="0"
name="MSearchResults" id="MSearchResults">
</iframe>
</div>
<div id="nav-path" class="navpath">
<ul>
<li class="navelem"><b>btllib</b></li><li class="navelem"><a class="el" href="classbtllib_1_1RollingHash.html">RollingHash</a></li> </ul>
</div>
</div><!-- top -->
<div class="header">
<div class="summary">
<a href="#pub-methods">Public Member Functions</a> |
<a href="#pro-methods">Protected Member Functions</a> |
<a href="#pro-attribs">Protected Attributes</a> |
<a href="classbtllib_1_1RollingHash-members.html">List of all members</a> </div>
<div class="headertitle">
<div class="title">btllib::RollingHash Class Reference</div> </div>
</div><!--header-->
<div class="contents">
<p><code>#include <<a class="el" href="rolling__hash_8hpp_source.html">rolling_hash.hpp</a>></code></p>
<div class="dynheader">
Inheritance diagram for btllib::RollingHash:</div>
<div class="dyncontent">
<div class="center">
<img src="classbtllib_1_1RollingHash.png" usemap="#btllib::RollingHash_map" alt=""/>
<map id="btllib::RollingHash_map" name="btllib::RollingHash_map">
<area href="classbtllib_1_1SeedRollingHash.html" alt="btllib::SeedRollingHash" shape="rect" coords="0,56,140,80"/>
</map>
</div></div>
<table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
Public Member Functions</h2></td></tr>
<tr class="memitem:a36e863f7d63bd1f1f4abbba0bc444ed9"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classbtllib_1_1RollingHash.html#a36e863f7d63bd1f1f4abbba0bc444ed9">RollingHash</a> (const char *seq, size_t seq_len, unsigned k, unsigned hash_num)</td></tr>
<tr class="separator:a36e863f7d63bd1f1f4abbba0bc444ed9"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a353201439e0ad2d5756c10446f5d9d1c"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classbtllib_1_1RollingHash.html#a353201439e0ad2d5756c10446f5d9d1c">RollingHash</a> (const std::string &seq, unsigned k, unsigned hash_num)</td></tr>
<tr class="separator:a353201439e0ad2d5756c10446f5d9d1c"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a49fd5e2e569084058d9548e851ed3b41"><td class="memItemLeft" align="right" valign="top"><a id="a49fd5e2e569084058d9548e851ed3b41"></a>
bool </td><td class="memItemRight" valign="bottom"><b>roll</b> ()</td></tr>
<tr class="separator:a49fd5e2e569084058d9548e851ed3b41"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a295b97e0f3d8cc400dce140a98dda053"><td class="memItemLeft" align="right" valign="top"><a id="a295b97e0f3d8cc400dce140a98dda053"></a>
const uint64_t * </td><td class="memItemRight" valign="bottom"><b>hashes</b> () const</td></tr>
<tr class="separator:a295b97e0f3d8cc400dce140a98dda053"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a5ef8b9f0a9a07c23acad18bab7fa881a"><td class="memItemLeft" align="right" valign="top"><a id="a5ef8b9f0a9a07c23acad18bab7fa881a"></a>
size_t </td><td class="memItemRight" valign="bottom"><b>get_pos</b> () const</td></tr>
<tr class="separator:a5ef8b9f0a9a07c23acad18bab7fa881a"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:acb65ffa3813214c9f2edad2c6db8d037"><td class="memItemLeft" align="right" valign="top"><a id="acb65ffa3813214c9f2edad2c6db8d037"></a>
unsigned </td><td class="memItemRight" valign="bottom"><b>get_k</b> () const</td></tr>
<tr class="separator:acb65ffa3813214c9f2edad2c6db8d037"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:af896887e64fc1f2d13f811b29fca2823"><td class="memItemLeft" align="right" valign="top"><a id="af896887e64fc1f2d13f811b29fca2823"></a>
unsigned </td><td class="memItemRight" valign="bottom"><b>get_hash_num</b> () const</td></tr>
<tr class="separator:af896887e64fc1f2d13f811b29fca2823"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pro-methods"></a>
Protected Member Functions</h2></td></tr>
<tr class="memitem:a17f81625791b89011d40ab591cdf2ea7"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classbtllib_1_1RollingHash.html#a17f81625791b89011d40ab591cdf2ea7">init</a> ()</td></tr>
<tr class="separator:a17f81625791b89011d40ab591cdf2ea7"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pro-attribs"></a>
Protected Attributes</h2></td></tr>
<tr class="memitem:a10237026164968818a44421d0587c62d"><td class="memItemLeft" align="right" valign="top"><a id="a10237026164968818a44421d0587c62d"></a>
const char * </td><td class="memItemRight" valign="bottom"><b>seq</b></td></tr>
<tr class="separator:a10237026164968818a44421d0587c62d"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a447e1ae4399619b04fa7842aa8dabd5e"><td class="memItemLeft" align="right" valign="top"><a id="a447e1ae4399619b04fa7842aa8dabd5e"></a>
const size_t </td><td class="memItemRight" valign="bottom"><b>seq_len</b></td></tr>
<tr class="separator:a447e1ae4399619b04fa7842aa8dabd5e"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a57abdbe8388cdaf789d947d627f29935"><td class="memItemLeft" align="right" valign="top"><a id="a57abdbe8388cdaf789d947d627f29935"></a>
const unsigned </td><td class="memItemRight" valign="bottom"><b>k</b></td></tr>
<tr class="separator:a57abdbe8388cdaf789d947d627f29935"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a70115d2d7225eff7c81d2f516018f4df"><td class="memItemLeft" align="right" valign="top"><a id="a70115d2d7225eff7c81d2f516018f4df"></a>
const unsigned </td><td class="memItemRight" valign="bottom"><b>hash_num</b></td></tr>
<tr class="separator:a70115d2d7225eff7c81d2f516018f4df"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a7a19ef6884a18b329a79a3914dbc77f4"><td class="memItemLeft" align="right" valign="top"><a id="a7a19ef6884a18b329a79a3914dbc77f4"></a>
size_t </td><td class="memItemRight" valign="bottom"><b>pos</b> = 0</td></tr>
<tr class="separator:a7a19ef6884a18b329a79a3914dbc77f4"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:af94af882e4579b9585a2b6ae9e62e334"><td class="memItemLeft" align="right" valign="top"><a id="af94af882e4579b9585a2b6ae9e62e334"></a>
std::vector< uint64_t > </td><td class="memItemRight" valign="bottom"><b>hashes_vector</b></td></tr>
<tr class="separator:af94af882e4579b9585a2b6ae9e62e334"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a3c92444f40afb8a2f30f80edfc71084d"><td class="memItemLeft" align="right" valign="top"><a id="a3c92444f40afb8a2f30f80edfc71084d"></a>
uint64_t </td><td class="memItemRight" valign="bottom"><b>forward_hash</b> = 0</td></tr>
<tr class="separator:a3c92444f40afb8a2f30f80edfc71084d"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:afad5cf99da83ff0fc52c65da446e5024"><td class="memItemLeft" align="right" valign="top"><a id="afad5cf99da83ff0fc52c65da446e5024"></a>
uint64_t </td><td class="memItemRight" valign="bottom"><b>reverse_hash</b> = 0</td></tr>
<tr class="separator:afad5cf99da83ff0fc52c65da446e5024"><td class="memSeparator" colspan="2"> </td></tr>
</table>
<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><p>Iterate over hash values for k-mers in a given DNA sequence.</p>
<p>This implementation uses ntHash function to efficiently calculate hash values for successive k-mers. </p>
</div><h2 class="groupheader">Constructor & Destructor Documentation</h2>
<a id="a36e863f7d63bd1f1f4abbba0bc444ed9"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a36e863f7d63bd1f1f4abbba0bc444ed9">◆ </a></span>RollingHash() <span class="overload">[1/2]</span></h2>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">btllib::RollingHash::RollingHash </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">size_t </td>
<td class="paramname"><em>seq_len</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">unsigned </td>
<td class="paramname"><em>k</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">unsigned </td>
<td class="paramname"><em>hash_num</em> </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>Constructor. </p><dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">seq</td><td>DNA sequence to be hashed </td></tr>
<tr><td class="paramname">seq_len</td><td>length of seq </td></tr>
<tr><td class="paramname">k</td><td>k-mer size </td></tr>
<tr><td class="paramname">hash_num</td><td>number of hashes </td></tr>
</table>
</dd>
</dl>
</div>
</div>
<a id="a353201439e0ad2d5756c10446f5d9d1c"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a353201439e0ad2d5756c10446f5d9d1c">◆ </a></span>RollingHash() <span class="overload">[2/2]</span></h2>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">btllib::RollingHash::RollingHash </td>
<td>(</td>
<td class="paramtype">const std::string & </td>
<td class="paramname"><em>seq</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">unsigned </td>
<td class="paramname"><em>k</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">unsigned </td>
<td class="paramname"><em>hash_num</em> </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>Constructor. </p><dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">seq</td><td>DNA sequence to be hashed </td></tr>
<tr><td class="paramname">k</td><td>k-mer size </td></tr>
<tr><td class="paramname">hash_num</td><td>number of hashes </td></tr>
</table>
</dd>
</dl>
</div>
</div>
<h2 class="groupheader">Member Function Documentation</h2>
<a id="a17f81625791b89011d40ab591cdf2ea7"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a17f81625791b89011d40ab591cdf2ea7">◆ </a></span>init()</h2>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">bool btllib::RollingHash::init </td>
<td>(</td>
<td class="paramname"></td><td>)</td>
<td></td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel">protected</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>Initialize internal state of iterator </p>
</div>
</div>
<hr/>The documentation for this class was generated from the following file:<ul>
<li>include/btllib/<a class="el" href="rolling__hash_8hpp_source.html">rolling_hash.hpp</a></li>
</ul>
</div><!-- contents -->
<!-- start footer part -->
<hr class="footer"/><address class="footer"><small>
Generated by  <a href="http://www.doxygen.org/index.html">
<img class="footer" src="doxygen.png" alt="doxygen"/>
</a> 1.8.17
</small></address>
</body>
</html>