← Back to branch summary

~ubuntu-branches/ubuntu/wily/openms/wily

« back to all changes in this revision

Viewing changes to doc/html/classOpenMS_1_1SuffixArrayTrypticSeqan-members.html

  • Committer: Package Import Robot
  • Author(s): Filippo Rusconi
  • Date: 2013-12-20 11:30:16 UTC
  • mfrom: (5.1.2 sid)
  • Revision ID: package-import@ubuntu.com-20131220113016-wre5g9bteeheq6he
Tags: 1.11.1-3
* remove version number from libbost development package names;
* ensure that AUTHORS is correctly shipped in all packages.

Show diffs side-by-side

added added

removed removed

Lines of Context:
doc/html/classOpenMS_1_1SuffixArrayTrypticSeqan-members.html
 
1
<HTML>
 
2
<HEAD>
 
3
<TITLE>Member List</TITLE>
 
4
<LINK HREF="doxygen.css" REL="stylesheet" TYPE="text/css">
 
5
<LINK HREF="style_ini.css" REL="stylesheet" TYPE="text/css">
 
6
</HEAD>
 
7
<BODY BGCOLOR="#FFFFFF">
 
8
<A href="index.html">Home</A> &nbsp;&middot;
 
9
<A href="classes.html">Classes</A> &nbsp;&middot;
 
10
<A href="annotated.html">Annotated Classes</A> &nbsp;&middot;
 
11
<A href="modules.html">Modules</A> &nbsp;&middot;
 
12
<A href="functions_func.html">Members</A> &nbsp;&middot;
 
13
<A href="namespaces.html">Namespaces</A> &nbsp;&middot;
 
14
<A href="pages.html">Related Pages</A>
 
15
<HR style="height:1px; border:none; border-top:1px solid #c0c0c0;">
 
16
<!-- Generated by Doxygen 1.8.5 -->
 
17
<div id="nav-path" class="navpath">
 
18
  <ul>
 
19
<li class="navelem"><a class="el" href="namespaceOpenMS.html">OpenMS</a></li><li class="navelem"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticSeqan.html">SuffixArrayTrypticSeqan</a></li>  </ul>
 
20
</div>
 
21
</div><!-- top -->
 
22
<div class="header">
 
23
  <div class="headertitle">
 
24
<div class="title">SuffixArrayTrypticSeqan Member List</div>  </div>
 
25
</div><!--header-->
 
26
<div class="contents">
 
27
 
 
28
<p>This is the complete list of members for <a class="el" href="classOpenMS_1_1SuffixArrayTrypticSeqan.html">SuffixArrayTrypticSeqan</a>, including all inherited members.</p>
 
29
<table class="directory">
 
30
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1WeightWrapper.html#aa0e0675e46f34052468f523f1c8aff2bab6f2220659ddcb84a0622d4aa4e0b112">AVERAGE</a> enum value</td><td class="entry"><a class="el" href="classOpenMS_1_1WeightWrapper.html">WeightWrapper</a></td><td class="entry"></td></tr>
 
31
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#af827429c64446f0d89d8d53f4029c63c">findFirst_</a>(const std::vector&lt; DoubleReal &gt; &amp;spec, DoubleReal &amp;m)</td><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html">SuffixArraySeqan</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
 
32
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#aceab577fe4e204ba7f9d260591c13b43">findFirst_</a>(const std::vector&lt; DoubleReal &gt; &amp;spec, DoubleReal &amp;m, SignedSize start, SignedSize end)</td><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html">SuffixArraySeqan</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
 
33
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#aa78cc1ec6532c467e25f892d1a649e1d">findSpec</a>(std::vector&lt; std::vector&lt; std::pair&lt; std::pair&lt; SignedSize, SignedSize &gt;, DoubleReal &gt; &gt; &gt; &amp;candidates, const std::vector&lt; DoubleReal &gt; &amp;spec)</td><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html">SuffixArraySeqan</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
 
34
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#a30dec5fbc364fa6168ef5c28d2ce988f">getNumberOfModifications</a>()</td><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html">SuffixArraySeqan</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
 
35
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#a35995e158ba0a000e682986f2ab57160">getTags</a>()</td><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html">SuffixArraySeqan</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
 
36
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#a8a62378185408f6af2e4349e6037b32a">getTolerance</a>() const </td><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html">SuffixArraySeqan</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
 
37
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#a65ab7ffcdc877e66b410aa4bc92935fb">getUseTags</a>()</td><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html">SuffixArraySeqan</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
 
38
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1WeightWrapper.html#af26fbe119eda2461447f2312786531f6">getWeight</a>(const AASequence &amp;aa) const </td><td class="entry"><a class="el" href="classOpenMS_1_1WeightWrapper.html">WeightWrapper</a></td><td class="entry"></td></tr>
 
39
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1WeightWrapper.html#a83b54901c7aa15994c0c665b8249e0f7">getWeight</a>(const EmpiricalFormula &amp;ef) const </td><td class="entry"><a class="el" href="classOpenMS_1_1WeightWrapper.html">WeightWrapper</a></td><td class="entry"></td></tr>
 
40
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1WeightWrapper.html#acf259e90e6852e4baab243bd5eff44e5">getWeight</a>(const Residue &amp;r, Residue::ResidueType res_type=Residue::Full) const </td><td class="entry"><a class="el" href="classOpenMS_1_1WeightWrapper.html">WeightWrapper</a></td><td class="entry"></td></tr>
 
41
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1WeightWrapper.html#a12c0a3ef8cbe7321db6724f92ba07730">getWeightMode</a>() const </td><td class="entry"><a class="el" href="classOpenMS_1_1WeightWrapper.html">WeightWrapper</a></td><td class="entry"></td></tr>
 
42
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#abc7e9c615867171906af75f497ac65f6">goNext_</a>(TIter &amp;it, DoubleReal &amp;m, std::stack&lt; DoubleReal &gt; &amp;allm, std::stack&lt; std::map&lt; DoubleReal, SignedSize &gt; &gt; &amp;mod_map)</td><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html">SuffixArraySeqan</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">protected</span></td></tr>
 
43
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#a8d5af4ff6cc3b745d142d15950196917">goNextSubTree_</a>(TIter &amp;it, DoubleReal &amp;m, std::stack&lt; DoubleReal &gt; &amp;allm, std::stack&lt; std::map&lt; DoubleReal, SignedSize &gt; &gt; &amp;mod_map)</td><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html">SuffixArraySeqan</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">protected</span></td></tr>
 
44
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#aab7a3c8279f06017689bc067db553866">goNextSubTree_</a>(TIter &amp;it)</td><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html">SuffixArraySeqan</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">protected</span></td></tr>
 
45
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#a4bcd335dc7db2067a36e380cc36e69db">index_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html">SuffixArraySeqan</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
 
46
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticSeqan.html#a9eedb3b9aa20ef87f387b54c9e7813d7">isDigestingEnd</a>(const char aa1, const char aa2) const </td><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticSeqan.html">SuffixArrayTrypticSeqan</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
 
47
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#a7f643787a8ddf761d7f96cc7890643d6">it_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html">SuffixArraySeqan</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
 
48
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#a82b500a04e1c860859dea2a5de81d486">masse_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html">SuffixArraySeqan</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
 
49
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1WeightWrapper.html#aa0e0675e46f34052468f523f1c8aff2ba3828195437a1112429b5c7a3e8780570">MONO</a> enum value</td><td class="entry"><a class="el" href="classOpenMS_1_1WeightWrapper.html">WeightWrapper</a></td><td class="entry"></td></tr>
 
50
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#afb270f403ee1906142ed086faddd9579">number_of_modifications_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html">SuffixArraySeqan</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
 
51
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#a439f6d35e3fe7db057e9bf13f42a2485">open</a>(const String &amp;filename)</td><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html">SuffixArraySeqan</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
 
52
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#af401425e4fadc7f9dae12bde81ed2ba4">parseTree_</a>(TIter &amp;it, std::vector&lt; std::pair&lt; SignedSize, SignedSize &gt; &gt; &amp;out_number, std::vector&lt; std::pair&lt; SignedSize, SignedSize &gt; &gt; &amp;edge_length, std::vector&lt; SignedSize &gt; &amp;leafe_depth)</td><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html">SuffixArraySeqan</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">protected</span></td></tr>
 
53
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#af51327da313f22aa8cb1abebb11cebe5">printStatistic</a>()</td><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html">SuffixArraySeqan</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
 
54
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#a28d5fa0a5f589e44cd18c30b6b6dbf63">s_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html">SuffixArraySeqan</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
 
55
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#af055ab1935e7aa87eb45534e2d26115c">save</a>(const String &amp;filename)</td><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html">SuffixArraySeqan</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
 
56
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#a04c30ff2f4f8f35549000277592c9e8d">setNumberOfModifications</a>(Size number_of_mods)</td><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html">SuffixArraySeqan</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
 
57
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#a89089f1b7138b71dfa5096c51367632b">setTags</a>(const std::vector&lt; OpenMS::String &gt; &amp;tags)</td><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html">SuffixArraySeqan</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
 
58
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#a946a09425e78f45c9cc2b921d72e8409">setTolerance</a>(DoubleReal t)</td><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html">SuffixArraySeqan</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
 
59
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#ab2650d016b9e7eaf4574d44817868f3d">setUseTags</a>(bool use_tags)</td><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html">SuffixArraySeqan</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
 
60
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1WeightWrapper.html#a86f49dcf25cd06d439db0390ae5604b5">setWeightMode</a>(const WEIGHTMODE mode)</td><td class="entry"><a class="el" href="classOpenMS_1_1WeightWrapper.html">WeightWrapper</a></td><td class="entry"></td></tr>
 
61
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1WeightWrapper.html#aa0e0675e46f34052468f523f1c8aff2ba4226c2437cbb49f44511f47e1bde3109">SIZE_OF_WEIGHTMODE</a> enum value</td><td class="entry"><a class="el" href="classOpenMS_1_1WeightWrapper.html">WeightWrapper</a></td><td class="entry"></td></tr>
 
62
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArray.html#abfdabd2b559c341d60a3a3979e81daaa">SuffixArray</a>(const String &amp;st, const String &amp;filename)</td><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArray.html">SuffixArray</a></td><td class="entry"></td></tr>
 
63
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArray.html#a4b1b30caafcf911c9e5b53d454fc3d42">SuffixArray</a>(const SuffixArray &amp;sa)</td><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArray.html">SuffixArray</a></td><td class="entry"></td></tr>
 
64
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArray.html#a7d57710f630ba50753236ec1860bc096">SuffixArray</a>()</td><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArray.html">SuffixArray</a></td><td class="entry"></td></tr>
 
65
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#a35a04b37e5b3a31a6bd2eab2596403c2">SuffixArraySeqan</a>(const String &amp;st, const String &amp;filename, const WeightWrapper::WEIGHTMODE weight_mode=WeightWrapper::MONO)</td><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html">SuffixArraySeqan</a></td><td class="entry"></td></tr>
 
66
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#a26dc50bfb537bb5cc0082a1481f54ff3">SuffixArraySeqan</a>(const SuffixArraySeqan &amp;source)</td><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html">SuffixArraySeqan</a></td><td class="entry"></td></tr>
 
67
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticSeqan.html#a10119b1df48bec175a8f4811b02bed25">SuffixArrayTrypticSeqan</a>(const String &amp;st, const String &amp;filename, const WeightWrapper::WEIGHTMODE weight_mode=WeightWrapper::MONO)</td><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticSeqan.html">SuffixArrayTrypticSeqan</a></td><td class="entry"></td></tr>
 
68
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#a26d1215083518387975aecec042c0fc0">tags_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html">SuffixArraySeqan</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
 
69
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#ad71c965ded7781aca71019c3873bc535">tol_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html">SuffixArraySeqan</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
 
70
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#ad146fa8579a5f8a876c4688cc5a68520">toString</a>()</td><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html">SuffixArraySeqan</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
 
71
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#a0a7158b249ff8c267b98581e56a584e3">use_tags_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html">SuffixArraySeqan</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
 
72
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1WeightWrapper.html#aa0e0675e46f34052468f523f1c8aff2b">WEIGHTMODE</a> enum name</td><td class="entry"><a class="el" href="classOpenMS_1_1WeightWrapper.html">WeightWrapper</a></td><td class="entry"></td></tr>
 
73
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1WeightWrapper.html#ad17dfc0067cbade3b4862477bb535c83">WeightWrapper</a>()</td><td class="entry"><a class="el" href="classOpenMS_1_1WeightWrapper.html">WeightWrapper</a></td><td class="entry"></td></tr>
 
74
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1WeightWrapper.html#a60ffdc2b9c2147851399c529b1a1fd51">WeightWrapper</a>(const WEIGHTMODE weight_mode)</td><td class="entry"><a class="el" href="classOpenMS_1_1WeightWrapper.html">WeightWrapper</a></td><td class="entry"></td></tr>
 
75
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1WeightWrapper.html#acf810b578f701801ea752d534d7fcbe9">WeightWrapper</a>(const WeightWrapper &amp;source)</td><td class="entry"><a class="el" href="classOpenMS_1_1WeightWrapper.html">WeightWrapper</a></td><td class="entry"></td></tr>
 
76
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArray.html#afa4acc59f254c5cb91963806dd8d9757">~SuffixArray</a>()=0</td><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArray.html">SuffixArray</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
 
77
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html#a4b0a33b865746aaefac892cf22de5832">~SuffixArraySeqan</a>()</td><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArraySeqan.html">SuffixArraySeqan</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
 
78
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1WeightWrapper.html#a0f2c08d0cebb514fee6ba050bb17aa0f">~WeightWrapper</a>()</td><td class="entry"><a class="el" href="classOpenMS_1_1WeightWrapper.html">WeightWrapper</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
 
79
</table></div><!-- contents -->
 
80
<HR style="height:1px; border:none; border-top:1px solid #c0c0c0;">
 
81
<TABLE width="100%" border="0">
 
82
<TR>
 
83
<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
 
84
<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:29 using doxygen 1.8.5</font></TD>
 
85
</TR>
 
86
</TABLE>
 
87
</BODY>
 
88
</HTML>