File: classOpenMS_1_1SuffixArrayTrypticCompressed-members.html

package info (click to toggle)
openms 1.11.1-5
links: PTS, VCS
area: main
in suites: jessie, jessie-kfreebsd
size: 436,688 kB
ctags: 150,907
sloc: cpp: 387,126; xml: 71,547; python: 7,764; ansic: 2,626; php: 2,499; sql: 737; ruby: 342; sh: 325; makefile: 128
file content (90 lines) | stat: -rw-r--r-- 19,639 bytes
<HTML>
<HEAD>
<TITLE>Member List</TITLE>
<LINK HREF="doxygen.css" REL="stylesheet" TYPE="text/css">
<LINK HREF="style_ini.css" REL="stylesheet" TYPE="text/css">
</HEAD>
<BODY BGCOLOR="#FFFFFF">
<A href="index.html">Home</A> &nbsp;&middot;
<A href="classes.html">Classes</A> &nbsp;&middot;
<A href="annotated.html">Annotated Classes</A> &nbsp;&middot;
<A href="modules.html">Modules</A> &nbsp;&middot;
<A href="functions_func.html">Members</A> &nbsp;&middot;
<A href="namespaces.html">Namespaces</A> &nbsp;&middot;
<A href="pages.html">Related Pages</A>
<HR style="height:1px; border:none; border-top:1px solid #c0c0c0;">
<!-- Generated by Doxygen 1.8.5 -->
<div id="nav-path" class="navpath">
  <ul>
<li class="navelem"><a class="el" href="namespaceOpenMS.html">OpenMS</a></li><li class="navelem"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html">SuffixArrayTrypticCompressed</a></li>  </ul>
</div>
</div><!-- top -->
<div class="header">
  <div class="headertitle">
<div class="title">SuffixArrayTrypticCompressed Member List</div>  </div>
</div><!--header-->
<div class="contents">

<p>This is the complete list of members for <a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html">SuffixArrayTrypticCompressed</a>, including all inherited members.</p>
<table class="directory">
  <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>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.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_1SuffixArrayTrypticCompressed.html">SuffixArrayTrypticCompressed</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.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_1SuffixArrayTrypticCompressed.html">SuffixArrayTrypticCompressed</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.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_1SuffixArrayTrypticCompressed.html">SuffixArrayTrypticCompressed</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html#ada568bc5db7aa43841ccb569d70f2770">getLCP_</a>(const std::pair&lt; SignedSize, SignedSize &gt; &amp;last_point, const std::pair&lt; SignedSize, SignedSize &gt; &amp;current_point)</td><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html">SuffixArrayTrypticCompressed</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html#ab81c8a6ba077713bc29f601b0515213c">getNextSep_</a>(const SignedSize p) const </td><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html">SuffixArrayTrypticCompressed</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html#a30dec5fbc364fa6168ef5c28d2ce988f">getNumberOfModifications</a>()</td><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html">SuffixArrayTrypticCompressed</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html#ad8e969d3476318682e49a4e03ec5ca80">getTags</a>()</td><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html">SuffixArrayTrypticCompressed</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html#a8a62378185408f6af2e4349e6037b32a">getTolerance</a>() const </td><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html">SuffixArrayTrypticCompressed</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html#a65ab7ffcdc877e66b410aa4bc92935fb">getUseTags</a>()</td><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html">SuffixArrayTrypticCompressed</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
  <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>
  <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>
  <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>
  <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>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html#a94a0dec6fde6ea6bd76d7af3b6a6ef85">hasMoreOutgoings_</a>(SignedSize start_index, SignedSize stop_index, SignedSize walked_in)</td><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html">SuffixArrayTrypticCompressed</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html#a7b7c9a1223f450c20d00cb8d4287c886">indices_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html">SuffixArrayTrypticCompressed</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html#a9eedb3b9aa20ef87f387b54c9e7813d7">isDigestingEnd</a>(const char aa1, const char aa2) const </td><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html">SuffixArrayTrypticCompressed</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html#ae059a0ce9b2655c414a8f450ecf69f8c">lcp_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html">SuffixArrayTrypticCompressed</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html#af61dba7387a69c804fdd6dda39c5a41c">masse_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html">SuffixArrayTrypticCompressed</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <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>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html#a5609ab550eb96c106ca2be458a149fcc">number_of_modifications_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html">SuffixArrayTrypticCompressed</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html#aae96c10617e1b87cb5a1960aa9855a49">open</a>(const String &amp;file_name)</td><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html">SuffixArrayTrypticCompressed</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html#a73b36bc7ca81bbdbfefe6447e9496c7e">parseTree_</a>(SignedSize start_index, SignedSize stop_index, SignedSize depth, SignedSize walked_in, SignedSize edge_len, 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_1SuffixArrayTrypticCompressed.html">SuffixArrayTrypticCompressed</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html#af51327da313f22aa8cb1abebb11cebe5">printStatistic</a>()</td><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html">SuffixArrayTrypticCompressed</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html#af98080eb757ac4ee1faa0c2b879a444f">progress_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html">SuffixArrayTrypticCompressed</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html#a28d5fa0a5f589e44cd18c30b6b6dbf63">s_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html">SuffixArrayTrypticCompressed</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html#a1c7203771149727e897bac6c1ce88a7f">save</a>(const String &amp;file_name)</td><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html">SuffixArrayTrypticCompressed</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html#a04c30ff2f4f8f35549000277592c9e8d">setNumberOfModifications</a>(Size number_of_mods)</td><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html">SuffixArrayTrypticCompressed</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html#a516052dbb7b4b3769779821175153957">setTags</a>(const std::vector&lt; String &gt; &amp;tags)</td><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html">SuffixArrayTrypticCompressed</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html#a946a09425e78f45c9cc2b921d72e8409">setTolerance</a>(DoubleReal t)</td><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html">SuffixArrayTrypticCompressed</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html#ab2650d016b9e7eaf4574d44817868f3d">setUseTags</a>(bool use_tags)</td><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html">SuffixArrayTrypticCompressed</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
  <tr><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>
  <tr class="even"><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>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html#a11613449679539b8daa4d52c0b4d7b0a">skip_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html">SuffixArrayTrypticCompressed</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <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>
  <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>
  <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>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html#a005ba5e318f32034cd5f071c87d6ebcf">SuffixArrayTrypticCompressed</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_1SuffixArrayTrypticCompressed.html">SuffixArrayTrypticCompressed</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html#a40a8df0b07863cd1d52a88778beca6f9">SuffixArrayTrypticCompressed</a>(const SuffixArrayTrypticCompressed &amp;sa)</td><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html">SuffixArrayTrypticCompressed</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html#a20ac87a76f2b6c24b00c1faf75b0dfa7">SuffixArrayTrypticCompressed</a>()</td><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html">SuffixArrayTrypticCompressed</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html#a26d1215083518387975aecec042c0fc0">tags_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html">SuffixArrayTrypticCompressed</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html#ad71c965ded7781aca71019c3873bc535">tol_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html">SuffixArrayTrypticCompressed</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html#ad146fa8579a5f8a876c4688cc5a68520">toString</a>()</td><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html">SuffixArrayTrypticCompressed</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html#a0a7158b249ff8c267b98581e56a584e3">use_tags_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html">SuffixArrayTrypticCompressed</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <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>
  <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>
  <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>
  <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>
  <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>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html#ad351cdd7a3b521fcbccd181988c5e09c">~SuffixArrayTrypticCompressed</a>()</td><td class="entry"><a class="el" href="classOpenMS_1_1SuffixArrayTrypticCompressed.html">SuffixArrayTrypticCompressed</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
  <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>
</table></div><!-- contents -->
<HR style="height:1px; border:none; border-top:1px solid #c0c0c0;">
<TABLE width="100%" border="0">
<TR>
<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:29 using doxygen 1.8.5</font></TD>
</TR>
</TABLE>
</BODY>
</HTML>