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  • Committer: Bazaar Package Importer
  • Author(s): Andres Salomon
  • Date: 2008-01-05 23:58:56 UTC
  • mfrom: (1.1.1 upstream)
  • Revision ID: james.westby@ubuntu.com-20080105235856-2kmxhxkz14qjy9ia
Tags: 3.5.0-1
* New upstream release.
* Add tcpp.dpatch.  This stops tests/stress/t.cpp from including
  ncbi_pch.hpp.  As far as I can tell, NCBI is not used at all, I have
  no idea where that came from..
* Silence some lintian warnings; binary-arch-rules-but-pkg-is-arch-indep
  and ancient-standards-version.

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html/a00104.html
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
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<html><head><meta http-equiv="Content-Type" content="text/html;charset=iso-8859-1">
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<title>BitMagic: bmconst.h Source File</title>
 
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<title>BitMagic: bm::gap_len_table&lt; T &gt; Struct Template Reference</title>
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<link href="doxygen.css" rel="stylesheet" type="text/css">
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</head><body>
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<!-- Generated by Doxygen 1.4.1 -->
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<div class="qindex"><a class="qindex" href="index.html">Main&nbsp;Page</a> | <a class="qindex" href="modules.html">Modules</a> | <a class="qindex" href="namespaces.html">Namespace List</a> | <a class="qindex" href="hierarchy.html">Class&nbsp;Hierarchy</a> | <a class="qindex" href="classes.html">Alphabetical&nbsp;List</a> | <a class="qindex" href="annotated.html">Data&nbsp;Structures</a> | <a class="qindex" href="dirs.html">Directories</a> | <a class="qindex" href="files.html">File&nbsp;List</a> | <a class="qindex" href="namespacemembers.html">Namespace&nbsp;Members</a> | <a class="qindex" href="functions.html">Data&nbsp;Fields</a> | <a class="qindex" href="globals.html">Globals</a> | <a class="qindex" href="examples.html">Examples</a></div>
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<div class="nav">
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<a class="el" href="dir_000000.html">src</a></div>
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<h1>bmconst.h</h1><a href="a00076.html">Go to the documentation of this file.</a><div class="fragment"><pre class="fragment">00001 <span class="comment">/*</span>
11
 
00002 <span class="comment">Copyright(c) 2002-2005 Anatoliy Kuznetsov(anatoliy_kuznetsov at yahoo.com)</span>
12
 
00003 <span class="comment"></span>
13
 
00004 <span class="comment">Permission is hereby granted, free of charge, to any person </span>
14
 
00005 <span class="comment">obtaining a copy of this software and associated documentation </span>
15
 
00006 <span class="comment">files (the "Software"), to deal in the Software without restriction, </span>
16
 
00007 <span class="comment">including without limitation the rights to use, copy, modify, merge, </span>
17
 
00008 <span class="comment">publish, distribute, sublicense, and/or sell copies of the Software, </span>
18
 
00009 <span class="comment">and to permit persons to whom the Software is furnished to do so, </span>
19
 
00010 <span class="comment">subject to the following conditions:</span>
20
 
00011 <span class="comment"></span>
21
 
00012 <span class="comment">The above copyright notice and this permission notice shall be included </span>
22
 
00013 <span class="comment">in all copies or substantial portions of the Software.</span>
23
 
00014 <span class="comment"></span>
24
 
00015 <span class="comment">THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, </span>
25
 
00016 <span class="comment">EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES </span>
26
 
00017 <span class="comment">OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. </span>
27
 
00018 <span class="comment">IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, </span>
28
 
00019 <span class="comment">DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, </span>
29
 
00020 <span class="comment">ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR </span>
30
 
00021 <span class="comment">OTHER DEALINGS IN THE SOFTWARE.</span>
31
 
00022 <span class="comment"></span>
32
 
00023 <span class="comment">For more information please visit:  http://bmagic.sourceforge.net</span>
33
 
00024 <span class="comment"></span>
34
 
00025 <span class="comment">*/</span>
35
 
00026 
36
 
00027 <span class="preprocessor">#ifndef BMCONST__H__INCLUDED__</span>
37
 
00028 <span class="preprocessor"></span><span class="preprocessor">#define BMCONST__H__INCLUDED__</span>
38
 
00029 <span class="preprocessor"></span>
39
 
00030 <span class="keyword">namespace </span>bm
40
 
00031 {
41
 
00032 
42
 
00033 <span class="preprocessor">#if defined(_WIN32) || defined (_WIN64)</span>
43
 
00034 <span class="preprocessor"></span>
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00035 <span class="keyword">typedef</span> <span class="keywordtype">unsigned</span> __int64 <a class="code" href="a00092.html#a8">id64_t</a>;
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00036 
46
 
00037 <span class="preprocessor">#else</span>
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00038 <span class="preprocessor"></span>
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<a name="l00039"></a><a class="code" href="a00092.html#a8">00039</a> <span class="keyword">typedef</span> <span class="keywordtype">unsigned</span> <span class="keywordtype">long</span> <span class="keywordtype">long</span> <a class="code" href="a00092.html#a8">id64_t</a>;
49
 
00040 
50
 
00041 <span class="preprocessor">#endif</span>
51
 
00042 <span class="preprocessor"></span>
52
 
<a name="l00043"></a><a class="code" href="a00092.html#a9">00043</a> <span class="keyword">typedef</span> <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span>   <a class="code" href="a00092.html#a9">id_t</a>;
53
 
<a name="l00044"></a><a class="code" href="a00092.html#a10">00044</a> <span class="keyword">typedef</span> <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span>   <a class="code" href="a00092.html#a10">word_t</a>;
54
 
<a name="l00045"></a><a class="code" href="a00092.html#a11">00045</a> <span class="keyword">typedef</span> <span class="keywordtype">unsigned</span> <span class="keywordtype">short</span> <a class="code" href="a00092.html#a11">short_t</a>;
55
 
00046 
56
 
00047 
57
 
00048 
58
 
<a name="l00049"></a><a class="code" href="a00092.html#a12">00049</a> <span class="keyword">const</span> <span class="keywordtype">unsigned</span> <a class="code" href="a00092.html#a12">id_max</a> = 0xFFFFFFFF;
59
 
00050 
60
 
00051 <span class="comment">// Data Block parameters</span>
61
 
00052 
62
 
<a name="l00053"></a><a class="code" href="a00092.html#a13">00053</a> <span class="keyword">const</span> <span class="keywordtype">unsigned</span> <a class="code" href="a00092.html#a13">set_block_size</a>  = 2048u;
63
 
<a name="l00054"></a><a class="code" href="a00092.html#a14">00054</a> <span class="keyword">const</span> <span class="keywordtype">unsigned</span> <a class="code" href="a00092.html#a14">set_block_shift</a> = 16u;
64
 
<a name="l00055"></a><a class="code" href="a00092.html#a15">00055</a> <span class="keyword">const</span> <span class="keywordtype">unsigned</span> <a class="code" href="a00092.html#a15">set_block_mask</a>  = 0xFFFFu;
65
 
<a name="l00056"></a><a class="code" href="a00092.html#a16">00056</a> <span class="keyword">const</span> <span class="keywordtype">unsigned</span> <a class="code" href="a00092.html#a16">set_blkblk_mask</a> = 0xFFFFFFu;
66
 
00057 
67
 
00058 <span class="comment">// Word parameters</span>
68
 
00059 
69
 
<a name="l00060"></a><a class="code" href="a00092.html#a17">00060</a> <span class="keyword">const</span> <span class="keywordtype">unsigned</span> <a class="code" href="a00092.html#a17">set_word_shift</a> = 5u;
70
 
<a name="l00061"></a><a class="code" href="a00092.html#a18">00061</a> <span class="keyword">const</span> <span class="keywordtype">unsigned</span> <a class="code" href="a00092.html#a18">set_word_mask</a>  = 0x1Fu;
71
 
00062 
72
 
00063 
73
 
00064 <span class="comment">// GAP related parameters.</span>
74
 
00065 
75
 
<a name="l00066"></a><a class="code" href="a00092.html#a19">00066</a> <span class="keyword">typedef</span> <span class="keywordtype">unsigned</span> <span class="keywordtype">short</span> <a class="code" href="a00092.html#a19">gap_word_t</a>;
76
 
00067 
77
 
<a name="l00068"></a><a class="code" href="a00092.html#a20">00068</a> <span class="keyword">const</span> <span class="keywordtype">unsigned</span> <a class="code" href="a00092.html#a20">gap_max_buff_len</a> = 1280;
78
 
<a name="l00069"></a><a class="code" href="a00092.html#a21">00069</a> <span class="keyword">const</span> <span class="keywordtype">unsigned</span> <a class="code" href="a00092.html#a21">gap_max_bits</a> = 65536;
79
 
<a name="l00070"></a><a class="code" href="a00092.html#a22">00070</a> <span class="keyword">const</span> <span class="keywordtype">unsigned</span> <a class="code" href="a00092.html#a22">gap_equiv_len</a> = 
80
 
00071    (<span class="keyword">sizeof</span>(bm::word_t) * bm::set_block_size) / <span class="keyword">sizeof</span>(<a class="code" href="a00092.html#a19">gap_word_t</a>);
81
 
<a name="l00072"></a><a class="code" href="a00092.html#a23">00072</a> <span class="keyword">const</span> <span class="keywordtype">unsigned</span> <a class="code" href="a00092.html#a23">gap_levels</a> = 4;
82
 
<a name="l00073"></a><a class="code" href="a00092.html#a24">00073</a> <span class="keyword">const</span> <span class="keywordtype">unsigned</span> <a class="code" href="a00092.html#a24">gap_max_level</a> = bm::gap_levels - 1;
83
 
00074 
84
 
00075 
85
 
00076 <span class="comment">// Block Array parameters</span>
86
 
00077 
87
 
<a name="l00078"></a><a class="code" href="a00092.html#a25">00078</a> <span class="keyword">const</span> <span class="keywordtype">unsigned</span> <a class="code" href="a00092.html#a25">set_array_size</a> = 256u;
88
 
<a name="l00079"></a><a class="code" href="a00092.html#a26">00079</a> <span class="keyword">const</span> <span class="keywordtype">unsigned</span> <a class="code" href="a00092.html#a26">set_array_shift</a> = 8u;
89
 
<a name="l00080"></a><a class="code" href="a00092.html#a27">00080</a> <span class="keyword">const</span> <span class="keywordtype">unsigned</span> <a class="code" href="a00092.html#a27">set_array_mask</a>  = 0xFFu;
90
 
<a name="l00081"></a><a class="code" href="a00092.html#a28">00081</a> <span class="keyword">const</span> <span class="keywordtype">unsigned</span> <a class="code" href="a00092.html#a28">set_total_blocks</a> = (bm::set_array_size * bm::set_array_size);
91
 
00082 
92
 
<a name="l00083"></a><a class="code" href="a00092.html#a29">00083</a> <span class="keyword">const</span> <span class="keywordtype">unsigned</span> <a class="code" href="a00092.html#a29">bits_in_block</a> = bm::set_block_size * <span class="keyword">sizeof</span>(bm::word_t) * 8;
93
 
<a name="l00084"></a><a class="code" href="a00092.html#a30">00084</a> <span class="keyword">const</span> <span class="keywordtype">unsigned</span> <a class="code" href="a00092.html#a30">bits_in_array</a> = bm::bits_in_block * bm::set_array_size;
94
 
00085 
95
 
00086 
96
 
00087 <span class="preprocessor">#ifdef BM64OPT</span>
97
 
00088 <span class="preprocessor"></span>
98
 
<a name="l00089"></a><a class="code" href="a00092.html#a31">00089</a> <span class="keyword">typedef</span> <a class="code" href="a00092.html#a8">id64_t</a>  <a class="code" href="a00092.html#a31">wordop_t</a>;
99
 
<a name="l00090"></a><a class="code" href="a00092.html#a32">00090</a> <span class="keyword">const</span> <a class="code" href="a00092.html#a8">id64_t</a>    <a class="code" href="a00092.html#a32">all_bits_mask</a> = 0xffffffffffffffff;
100
 
00091 
101
 
<a name="l00092"></a><a class="code" href="a00076.html#a0">00092</a> <span class="preprocessor"># define DECLARE_TEMP_BLOCK(x)  bm::id64_t x[bm::set_block_size / 2]; </span>
102
 
<a name="l00093"></a><a class="code" href="a00092.html#a33">00093</a> <span class="preprocessor"></span><span class="keyword">const</span> <span class="keywordtype">unsigned</span> <a class="code" href="a00092.html#a33">set_block_size_op</a>  = bm::set_block_size / 2;
103
 
00094 
104
 
00095 
105
 
00096 <span class="preprocessor">#else</span>
106
 
00097 <span class="preprocessor"></span>
107
 
00098 <span class="keyword">typedef</span> <a class="code" href="a00092.html#a10">word_t</a> <a class="code" href="a00092.html#a31">wordop_t</a>;
108
 
00099 <span class="keyword">const</span> <a class="code" href="a00092.html#a10">word_t</a> <a class="code" href="a00092.html#a32">all_bits_mask</a> = 0xffffffff;
109
 
00100 
110
 
00101 <span class="preprocessor"># define DECLARE_TEMP_BLOCK(x)  unsigned x[bm::set_block_size]; </span>
111
 
00102 <span class="preprocessor"></span><span class="keyword">const</span> <span class="keywordtype">unsigned</span> <a class="code" href="a00092.html#a33">set_block_size_op</a>  = bm::set_block_size;
112
 
00103 
113
 
00104 <span class="preprocessor">#endif</span>
114
 
00105 <span class="preprocessor"></span>
115
 
00106 
116
 
00107 <span class="comment"></span>
117
 
00108 <span class="comment">/*!</span>
118
 
00109 <span class="comment">   @brief Block allocation strategies.</span>
119
 
00110 <span class="comment">   @ingroup bvector</span>
120
 
00111 <span class="comment">*/</span>
121
 
<a name="l00112"></a><a class="code" href="a00095.html#ga0">00112</a> <span class="keyword">enum</span> strategy
122
 
00113 {
123
 
00114     BM_BIT = 0, <span class="comment">//!&lt; No GAP compression strategy. All new blocks are bit blocks.</span>
124
 
00115 <span class="comment"></span>    BM_GAP = 1  <span class="comment">//!&lt; GAP compression is ON.</span>
125
 
00116 <span class="comment"></span>};
126
 
00117 
127
 
00118 
128
 
00119 } <span class="comment">// namespace</span>
129
 
00120 
130
 
00121 <span class="preprocessor">#endif</span>
131
 
00122 <span class="preprocessor"></span>
132
 
</pre></div><hr size="1"><address style="align: right;"><small>Generated on Thu Apr 20 13:28:46 2006 for BitMagic by&nbsp;
 
9
<a class="el" href="a00129.html">bm</a>::<a class="el" href="a00104.html">gap_len_table</a></div>
 
10
<h1>bm::gap_len_table&lt; T &gt; Struct Template Reference<br>
 
11
<small>
 
12
[<a class="el" href="a00133.html">GAP functions</a>]</small>
 
13
</h1>Default GAP lengths table.  
 
14
<a href="#_details">More...</a>
 
15
<p>
 
16
<code>#include &lt;<a class="el" href="a00141.html">bmfunc.h</a>&gt;</code>
 
17
<p>
 
18
<table border="0" cellpadding="0" cellspacing="0">
 
19
<tr><td></td></tr>
 
20
<tr><td colspan="2"><br><h2>Static Public Attributes</h2></td></tr>
 
21
<tr><td class="memItemLeft" nowrap align="right" valign="top">static const <a class="el" href="a00129.html#a36">gap_word_t</a>&nbsp;</td><td class="memItemRight" valign="bottom"><a class="el" href="a00104.html#s0">_len</a> [<a class="el" href="a00129.html#a40">bm::gap_levels</a>]</td></tr>
 
22
 
 
23
</table>
 
24
<hr><a name="_details"></a><h2>Detailed Description</h2>
 
25
<h3>template&lt;bool T&gt;<br>
 
26
 struct bm::gap_len_table&lt; T &gt;</h3>
 
27
 
 
28
Default GAP lengths table. 
 
29
<p>
 
30
 
 
31
<p>
 
32
Definition at line <a class="el" href="a00141.html#l00100">100</a> of file <a class="el" href="a00141.html">bmfunc.h</a>.<hr><h2>Field Documentation</h2>
 
33
<a class="anchor" name="s0" doxytag="bm::gap_len_table::_len"></a><p>
 
34
<table class="mdTable" cellpadding="2" cellspacing="0">
 
35
  <tr>
 
36
    <td class="mdRow">
 
37
      <table cellpadding="0" cellspacing="0" border="0">
 
38
        <tr>
 
39
          <td class="mdPrefix" colspan="4">
 
40
template&lt;bool T&gt; </td>
 
41
        </tr>
 
42
        <tr>
 
43
          <td class="md" nowrap valign="top">const <a class="el" href="a00129.html#a36">gap_word_t</a> <a class="el" href="a00104.html">bm::gap_len_table</a>&lt; T &gt;::<a class="el" href="a00104.html#s0">_len</a><code> [static]</code>          </td>
 
44
        </tr>
 
45
      </table>
 
46
    </td>
 
47
  </tr>
 
48
</table>
 
49
<table cellspacing="5" cellpadding="0" border="0">
 
50
  <tr>
 
51
    <td>
 
52
      &nbsp;
 
53
    </td>
 
54
    <td>
 
55
 
 
56
<p>
 
57
<b>Initial value:</b><div class="fragment"><pre class="fragment"> 
 
58
                { 128, 256, 512, bm::gap_max_buff_len }
 
59
</pre></div>
 
60
<p>
 
61
Definition at line <a class="el" href="a00141.html#l00106">106</a> of file <a class="el" href="a00141.html">bmfunc.h</a>.    </td>
 
62
  </tr>
 
63
</table>
 
64
<hr>The documentation for this struct was generated from the following file:<ul>
 
65
<li><a class="el" href="a00141.html">bmfunc.h</a></ul>
 
66
<hr size="1"><address style="align: right;"><small>Generated on Sun Aug 5 14:12:40 2007 for BitMagic by&nbsp;
133
67
<a href="http://www.doxygen.org/index.html">
134
68
<img src="doxygen.png" alt="doxygen" align="middle" border="0"></a> 1.4.1 </small></address>
135
69
</body>