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  • 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.

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doc/html/classOpenMS_1_1PrecursorIonSelection.html
 
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<HTML>
 
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<HEAD>
 
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<TITLE>PrecursorIonSelection Class Reference</TITLE>
 
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<LINK HREF="doxygen.css" REL="stylesheet" TYPE="text/css">
 
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<BODY BGCOLOR="#FFFFFF">
 
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<A href="index.html">Home</A> &nbsp;&middot;
 
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<A href="classes.html">Classes</A> &nbsp;&middot;
 
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<A href="annotated.html">Annotated Classes</A> &nbsp;&middot;
 
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<A href="modules.html">Modules</A> &nbsp;&middot;
 
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<A href="functions_func.html">Members</A> &nbsp;&middot;
 
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<A href="namespaces.html">Namespaces</A> &nbsp;&middot;
 
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<A href="pages.html">Related Pages</A>
 
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<HR style="height:1px; border:none; border-top:1px solid #c0c0c0;">
 
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<div id="nav-path" class="navpath">
 
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  <ul>
 
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<li class="navelem"><a class="el" href="namespaceOpenMS.html">OpenMS</a></li><li class="navelem"><a class="el" href="classOpenMS_1_1PrecursorIonSelection.html">PrecursorIonSelection</a></li>  </ul>
 
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</div>
 
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<div class="header">
 
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  <div class="summary">
 
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<a href="#nested-classes">Classes</a> &#124;
 
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<a href="#pub-types">Public Types</a> &#124;
 
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<a href="#pub-methods">Public Member Functions</a> &#124;
 
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<a href="#pri-methods">Private Member Functions</a> &#124;
 
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<a href="#pri-attribs">Private Attributes</a> &#124;
 
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<a href="classOpenMS_1_1PrecursorIonSelection-members.html">List of all members</a>  </div>
 
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  <div class="headertitle">
 
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<div class="title">PrecursorIonSelection Class Reference</div>  </div>
 
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</div><!--header-->
 
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<div class="contents">
 
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<p>This class implements different precursor ion selection strategies.  
 
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 <a href="classOpenMS_1_1PrecursorIonSelection.html#details">More...</a></p>
 
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<p><code>#include &lt;<a class="el" href="PrecursorIonSelection_8h_source.html">OpenMS/ANALYSIS/TARGETED/PrecursorIonSelection.h</a>&gt;</code></p>
 
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<div class="dynheader">
 
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Inheritance diagram for PrecursorIonSelection:</div>
 
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 <div class="center">
 
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  <img src="classOpenMS_1_1PrecursorIonSelection.png" usemap="#PrecursorIonSelection_map" alt=""/>
 
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  <map id="PrecursorIonSelection_map" name="PrecursorIonSelection_map">
 
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<area href="classOpenMS_1_1DefaultParamHandler.html" title="A base class for all classes handling default parameters. " alt="DefaultParamHandler" shape="rect" coords="0,0,138,24"/>
 
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</map>
 
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 </div></div>
 
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<table class="memberdecls">
 
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="nested-classes"></a>
 
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Classes</h2></td></tr>
 
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<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">struct &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structOpenMS_1_1PrecursorIonSelection_1_1SeqTotalScoreMore.html">SeqTotalScoreMore</a></td></tr>
 
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<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight">Compare by score.  <a href="structOpenMS_1_1PrecursorIonSelection_1_1SeqTotalScoreMore.html#details">More...</a><br/></td></tr>
 
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<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">struct &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structOpenMS_1_1PrecursorIonSelection_1_1TotalScoreMore.html">TotalScoreMore</a></td></tr>
 
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<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight">Compare by score.  <a href="structOpenMS_1_1PrecursorIonSelection_1_1TotalScoreMore.html#details">More...</a><br/></td></tr>
 
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<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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</table><table class="memberdecls">
 
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-types"></a>
 
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Public Types</h2></td></tr>
 
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<tr class="memitem:a1d1cfd8ffb84e947f82999c682b666a7"><td class="memItemLeft" align="right" valign="top">enum &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PrecursorIonSelection.html#a1d1cfd8ffb84e947f82999c682b666a7">Type</a> { <br/>
 
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&#160;&#160;<a class="el" href="classOpenMS_1_1PrecursorIonSelection.html#a1d1cfd8ffb84e947f82999c682b666a7aafb6828f5a8b8b40648e96ce2e5f435b">IPS</a>, 
 
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<a class="el" href="classOpenMS_1_1PrecursorIonSelection.html#a1d1cfd8ffb84e947f82999c682b666a7a241370a8eee3fc0070dce7c2cc8da0b6">ILP_IPS</a>, 
 
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<a class="el" href="classOpenMS_1_1PrecursorIonSelection.html#a1d1cfd8ffb84e947f82999c682b666a7a38aefbb94f63c43b1c8047151c83ca64">SPS</a>, 
 
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<a class="el" href="classOpenMS_1_1PrecursorIonSelection.html#a1d1cfd8ffb84e947f82999c682b666a7aa58d945ae9279992a5a9a1e908b770cb">UPSHIFT</a>, 
 
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<br/>
 
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&#160;&#160;<a class="el" href="classOpenMS_1_1PrecursorIonSelection.html#a1d1cfd8ffb84e947f82999c682b666a7a3ad159e1881c0b9db5274d155c9faf28">DOWNSHIFT</a>, 
 
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<a class="el" href="classOpenMS_1_1PrecursorIonSelection.html#a1d1cfd8ffb84e947f82999c682b666a7afd8b47cd00ea3ad6c3c275e1ffcce606">DEX</a>
 
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<br/>
 
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 }</td></tr>
 
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<tr class="memdesc:a1d1cfd8ffb84e947f82999c682b666a7"><td class="mdescLeft">&#160;</td><td class="mdescRight"><a class="el" href="classOpenMS_1_1Precursor.html" title="Precursor meta information. ">Precursor</a> ion selection type (iterative, static, upshift, downshift, dynamic exclusion).  <a href="classOpenMS_1_1PrecursorIonSelection.html#a1d1cfd8ffb84e947f82999c682b666a7">More...</a><br/></td></tr>
 
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<tr class="separator:a1d1cfd8ffb84e947f82999c682b666a7"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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</table><table class="memberdecls">
 
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
 
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Public Member Functions</h2></td></tr>
 
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<tr class="memitem:ac48bbb4aaf4fb10469d05f954810c67d"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PrecursorIonSelection.html#ac48bbb4aaf4fb10469d05f954810c67d">PrecursorIonSelection</a> ()</td></tr>
 
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<tr class="separator:ac48bbb4aaf4fb10469d05f954810c67d"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<tr class="memitem:a2d3d5a0fafc2571f619b2feb66505b2c"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PrecursorIonSelection.html#a2d3d5a0fafc2571f619b2feb66505b2c">PrecursorIonSelection</a> (const <a class="el" href="classOpenMS_1_1PrecursorIonSelection.html">PrecursorIonSelection</a> &amp;source)</td></tr>
 
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<tr class="separator:a2d3d5a0fafc2571f619b2feb66505b2c"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<tr class="memitem:a339727faeacb33d458239e23e6f38a5c"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PrecursorIonSelection.html#a339727faeacb33d458239e23e6f38a5c">~PrecursorIonSelection</a> ()</td></tr>
 
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<tr class="separator:a339727faeacb33d458239e23e6f38a5c"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<tr class="memitem:a136d8fee61d49118a5203b54fa621ea0"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PrecursorIonSelection.html#a136d8fee61d49118a5203b54fa621ea0">getMaxScore</a> () const </td></tr>
 
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<tr class="separator:a136d8fee61d49118a5203b54fa621ea0"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<tr class="memitem:ad3a5be860a268a2fa37776730d91fbc9"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PrecursorIonSelection.html#ad3a5be860a268a2fa37776730d91fbc9">setMaxScore</a> (const <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> &amp;max_score)</td></tr>
 
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<tr class="separator:ad3a5be860a268a2fa37776730d91fbc9"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<tr class="memitem:a2c348a002bfdedc62091f660a1dc2ad3"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PrecursorIonSelection.html#a2c348a002bfdedc62091f660a1dc2ad3">sortByTotalScore</a> (<a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a>&lt;&gt; &amp;features)</td></tr>
 
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<tr class="memdesc:a2c348a002bfdedc62091f660a1dc2ad3"><td class="mdescLeft">&#160;</td><td class="mdescRight">Sort features by total score.  <a href="#a2c348a002bfdedc62091f660a1dc2ad3">More...</a><br/></td></tr>
 
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<tr class="separator:a2c348a002bfdedc62091f660a1dc2ad3"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<tr class="memitem:acaecf1b0ad521b2841e6946d9608db7b"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PrecursorIonSelection.html#acaecf1b0ad521b2841e6946d9608db7b">getNextPrecursors</a> (<a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a>&lt;&gt; &amp;features, <a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a>&lt;&gt; &amp;next_features, <a class="el" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a> number)</td></tr>
 
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<tr class="memdesc:acaecf1b0ad521b2841e6946d9608db7b"><td class="mdescLeft">&#160;</td><td class="mdescRight">Returns features with highest score for MS/MS.  <a href="#acaecf1b0ad521b2841e6946d9608db7b">More...</a><br/></td></tr>
 
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<tr class="separator:acaecf1b0ad521b2841e6946d9608db7b"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<tr class="memitem:a32956b1163d1167a2d326f2cc441de90"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PrecursorIonSelection.html#a32956b1163d1167a2d326f2cc441de90">getNextPrecursorsSeq</a> (<a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a>&lt;&gt; &amp;features, <a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a>&lt;&gt; &amp;next_features, <a class="el" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a> number, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> &amp;rt)</td></tr>
 
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<tr class="separator:a32956b1163d1167a2d326f2cc441de90"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<tr class="memitem:a1617e594e09d4f445de0ee207e13d4e1"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PrecursorIonSelection.html#a1617e594e09d4f445de0ee207e13d4e1">getNextPrecursors</a> (std::vector&lt; <a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> &gt; &amp;solution_indices, std::vector&lt; <a class="el" href="structOpenMS_1_1PSLPFormulation_1_1IndexTriple.html">PSLPFormulation::IndexTriple</a> &gt; &amp;variable_indices, std::set&lt; <a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> &gt; &amp;measured_variables, <a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a>&lt;&gt; &amp;features, <a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a>&lt;&gt; &amp;new_features, <a class="el" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a> step_size, <a class="el" href="classOpenMS_1_1PSLPFormulation.html">PSLPFormulation</a> &amp;ilp)</td></tr>
 
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<tr class="separator:a1617e594e09d4f445de0ee207e13d4e1"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<tr class="memitem:aea9e9fe1f13d14873c765ddec8f38150"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PrecursorIonSelection.html#aea9e9fe1f13d14873c765ddec8f38150">rescore</a> (<a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a>&lt;&gt; &amp;features, std::vector&lt; <a class="el" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> &gt; &amp;new_pep_ids, std::vector&lt; <a class="el" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a> &gt; &amp;prot_ids, <a class="el" href="classOpenMS_1_1PrecursorIonSelectionPreprocessing.html">PrecursorIonSelectionPreprocessing</a> &amp;preprocessed_db, bool check_meta_values=true)</td></tr>
 
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<tr class="memdesc:aea9e9fe1f13d14873c765ddec8f38150"><td class="mdescLeft">&#160;</td><td class="mdescRight">Change scoring of features using peptide identifications only from spectra of the last iteration.  <a href="#aea9e9fe1f13d14873c765ddec8f38150">More...</a><br/></td></tr>
 
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<tr class="separator:aea9e9fe1f13d14873c765ddec8f38150"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<tr class="memitem:a990b40a17cf86c4b1f3f8d081a9c77c5"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PrecursorIonSelection.html#a990b40a17cf86c4b1f3f8d081a9c77c5">simulateRun</a> (<a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a>&lt;&gt; &amp;features, std::vector&lt; <a class="el" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> &gt; &amp;pep_ids, std::vector&lt; <a class="el" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a> &gt; &amp;prot_ids, <a class="el" href="classOpenMS_1_1PrecursorIonSelectionPreprocessing.html">PrecursorIonSelectionPreprocessing</a> &amp;preprocessed_db, <a class="el" href="classOpenMS_1_1String.html">String</a> path, <a class="el" href="classOpenMS_1_1MSExperiment.html">MSExperiment</a>&lt;&gt; &amp;experiment, <a class="el" href="classOpenMS_1_1String.html">String</a> precursor_path=&quot;&quot;)</td></tr>
 
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<tr class="memdesc:a990b40a17cf86c4b1f3f8d081a9c77c5"><td class="mdescLeft">&#160;</td><td class="mdescRight">Simulate the iterative precursor ion selection.  <a href="#a990b40a17cf86c4b1f3f8d081a9c77c5">More...</a><br/></td></tr>
 
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<tr class="separator:a990b40a17cf86c4b1f3f8d081a9c77c5"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<tr class="memitem:a2b206fdbe8649b90b854129f37fc594a"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PrecursorIonSelection.html#a2b206fdbe8649b90b854129f37fc594a">setLPSolver</a> (<a class="el" href="classOpenMS_1_1LPWrapper.html#ab659f8690ca779b8c3d73fe524a39a00">LPWrapper::SOLVER</a> solver)</td></tr>
 
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<tr class="separator:a2b206fdbe8649b90b854129f37fc594a"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<tr class="memitem:ac945a0966726a3a644d194b81c28d960"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1LPWrapper.html#ab659f8690ca779b8c3d73fe524a39a00">LPWrapper::SOLVER</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PrecursorIonSelection.html#ac945a0966726a3a644d194b81c28d960">getLPSolver</a> ()</td></tr>
 
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<tr class="separator:ac945a0966726a3a644d194b81c28d960"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<tr class="memitem:ad20897c5c8bd47f5d4005989bead0e55"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PrecursorIonSelection.html#ad20897c5c8bd47f5d4005989bead0e55">reset</a> ()</td></tr>
 
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<tr class="separator:ad20897c5c8bd47f5d4005989bead0e55"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<tr class="memitem:add0a01651d44ed438fd2d9202013c2b4"><td class="memItemLeft" align="right" valign="top">const std::map&lt; <a class="el" href="classOpenMS_1_1String.html">String</a>, <br class="typebreak"/>
 
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std::set&lt; <a class="el" href="classOpenMS_1_1String.html">String</a> &gt; &gt; &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PrecursorIonSelection.html#add0a01651d44ed438fd2d9202013c2b4">getPeptideProteinCounter</a> ()</td></tr>
 
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<tr class="separator:add0a01651d44ed438fd2d9202013c2b4"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<tr class="inherit_header pub_methods_classOpenMS_1_1DefaultParamHandler"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_classOpenMS_1_1DefaultParamHandler')"><img src="closed.png" alt="-"/>&#160;Public Member Functions inherited from <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td></tr>
 
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<tr class="memitem:afb6802fda161cb0c1a4a05597f94aecc inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#afb6802fda161cb0c1a4a05597f94aecc">DefaultParamHandler</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;name)</td></tr>
 
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<tr class="memdesc:afb6802fda161cb0c1a4a05597f94aecc inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft">&#160;</td><td class="mdescRight">Constructor with name that is displayed in error messages.  <a href="#afb6802fda161cb0c1a4a05597f94aecc">More...</a><br/></td></tr>
 
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<tr class="separator:afb6802fda161cb0c1a4a05597f94aecc inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<tr class="memitem:a954da7eef3cfddda446574eaadd20abb inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a954da7eef3cfddda446574eaadd20abb">DefaultParamHandler</a> (const <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a> &amp;rhs)</td></tr>
 
115
<tr class="memdesc:a954da7eef3cfddda446574eaadd20abb inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft">&#160;</td><td class="mdescRight">Copy constructor.  <a href="#a954da7eef3cfddda446574eaadd20abb">More...</a><br/></td></tr>
 
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<tr class="separator:a954da7eef3cfddda446574eaadd20abb inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<tr class="memitem:a11e9d6dd34fe8860874aa8abe0ec121b inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">virtual&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a11e9d6dd34fe8860874aa8abe0ec121b">~DefaultParamHandler</a> ()</td></tr>
 
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<tr class="memdesc:a11e9d6dd34fe8860874aa8abe0ec121b inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft">&#160;</td><td class="mdescRight">Destructor.  <a href="#a11e9d6dd34fe8860874aa8abe0ec121b">More...</a><br/></td></tr>
 
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<tr class="separator:a11e9d6dd34fe8860874aa8abe0ec121b inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<tr class="memitem:ae6b6d68036a573a44f6609460ba2dfb6 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">virtual <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#ae6b6d68036a573a44f6609460ba2dfb6">operator=</a> (const <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a> &amp;rhs)</td></tr>
 
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<tr class="memdesc:ae6b6d68036a573a44f6609460ba2dfb6 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft">&#160;</td><td class="mdescRight">Assignment operator.  <a href="#ae6b6d68036a573a44f6609460ba2dfb6">More...</a><br/></td></tr>
 
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<tr class="separator:ae6b6d68036a573a44f6609460ba2dfb6 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<tr class="memitem:ac435f2dd4d9f9328db83af97129a8d7e inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">virtual bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#ac435f2dd4d9f9328db83af97129a8d7e">operator==</a> (const <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a> &amp;rhs) const </td></tr>
 
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<tr class="memdesc:ac435f2dd4d9f9328db83af97129a8d7e inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft">&#160;</td><td class="mdescRight">Equality operator.  <a href="#ac435f2dd4d9f9328db83af97129a8d7e">More...</a><br/></td></tr>
 
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<tr class="separator:ac435f2dd4d9f9328db83af97129a8d7e inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<tr class="memitem:abc8067511cfc949ae942ea2b08588f81 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#abc8067511cfc949ae942ea2b08588f81">setParameters</a> (const <a class="el" href="classOpenMS_1_1Param.html">Param</a> &amp;param)</td></tr>
 
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<tr class="memdesc:abc8067511cfc949ae942ea2b08588f81 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft">&#160;</td><td class="mdescRight">Sets the parameters.  <a href="#abc8067511cfc949ae942ea2b08588f81">More...</a><br/></td></tr>
 
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<tr class="separator:abc8067511cfc949ae942ea2b08588f81 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<tr class="memitem:a7f6aab5a7dfbdd1c062a4352a29361f3 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classOpenMS_1_1Param.html">Param</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a7f6aab5a7dfbdd1c062a4352a29361f3">getParameters</a> () const </td></tr>
 
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<tr class="memdesc:a7f6aab5a7dfbdd1c062a4352a29361f3 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft">&#160;</td><td class="mdescRight">Non-mutable access to the parameters.  <a href="#a7f6aab5a7dfbdd1c062a4352a29361f3">More...</a><br/></td></tr>
 
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<tr class="separator:a7f6aab5a7dfbdd1c062a4352a29361f3 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<tr class="memitem:a02f02fa9832ca3e8d47c575a39803a2a inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classOpenMS_1_1Param.html">Param</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a02f02fa9832ca3e8d47c575a39803a2a">getDefaults</a> () const </td></tr>
 
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<tr class="memdesc:a02f02fa9832ca3e8d47c575a39803a2a inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft">&#160;</td><td class="mdescRight">Non-mutable access to the default parameters.  <a href="#a02f02fa9832ca3e8d47c575a39803a2a">More...</a><br/></td></tr>
 
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<tr class="separator:a02f02fa9832ca3e8d47c575a39803a2a inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<tr class="memitem:aaee0f2845288173de9f6ad47e6ad31d5 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#aaee0f2845288173de9f6ad47e6ad31d5">getName</a> () const </td></tr>
 
136
<tr class="memdesc:aaee0f2845288173de9f6ad47e6ad31d5 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft">&#160;</td><td class="mdescRight">Non-mutable access to the name.  <a href="#aaee0f2845288173de9f6ad47e6ad31d5">More...</a><br/></td></tr>
 
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<tr class="separator:aaee0f2845288173de9f6ad47e6ad31d5 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<tr class="memitem:a77d37f2e1c12e8bd33ea0e660a89e927 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a77d37f2e1c12e8bd33ea0e660a89e927">setName</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;name)</td></tr>
 
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<tr class="memdesc:a77d37f2e1c12e8bd33ea0e660a89e927 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft">&#160;</td><td class="mdescRight">Mutable access to the name.  <a href="#a77d37f2e1c12e8bd33ea0e660a89e927">More...</a><br/></td></tr>
 
140
<tr class="separator:a77d37f2e1c12e8bd33ea0e660a89e927 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<tr class="memitem:a768d4a2093627a2f34728656a9721bdf inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">const std::vector&lt; <a class="el" href="classOpenMS_1_1String.html">String</a> &gt; &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a768d4a2093627a2f34728656a9721bdf">getSubsections</a> () const </td></tr>
 
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<tr class="memdesc:a768d4a2093627a2f34728656a9721bdf inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft">&#160;</td><td class="mdescRight">Non-mutable access to the registered subsections.  <a href="#a768d4a2093627a2f34728656a9721bdf">More...</a><br/></td></tr>
 
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<tr class="separator:a768d4a2093627a2f34728656a9721bdf inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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</table><table class="memberdecls">
 
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pri-methods"></a>
 
146
Private Member Functions</h2></td></tr>
 
147
<tr class="memitem:a6d925990e26343cecf35b765b3ee8eda"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PrecursorIonSelection.html#a6d925990e26343cecf35b765b3ee8eda">simulateILPBasedIPSRun_</a> (<a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a>&lt;&gt; &amp;features, <a class="el" href="classOpenMS_1_1MSExperiment.html">MSExperiment</a>&lt;&gt; &amp;experiment, std::vector&lt; <a class="el" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> &gt; &amp;pep_ids, std::vector&lt; <a class="el" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a> &gt; &amp;prot_ids, <a class="el" href="classOpenMS_1_1PrecursorIonSelectionPreprocessing.html">PrecursorIonSelectionPreprocessing</a> &amp;preprocessed_db, <a class="el" href="classOpenMS_1_1String.html">String</a> output_path, <a class="el" href="classOpenMS_1_1String.html">String</a> precursor_path=&quot;&quot;)</td></tr>
 
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<tr class="separator:a6d925990e26343cecf35b765b3ee8eda"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<tr class="memitem:acb2e29dc60d50478abfdf1c85de60b37"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PrecursorIonSelection.html#acb2e29dc60d50478abfdf1c85de60b37">simulateRun_</a> (<a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a>&lt;&gt; &amp;features, std::vector&lt; <a class="el" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> &gt; &amp;pep_ids, std::vector&lt; <a class="el" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a> &gt; &amp;prot_ids, <a class="el" href="classOpenMS_1_1PrecursorIonSelectionPreprocessing.html">PrecursorIonSelectionPreprocessing</a> &amp;preprocessed_db, <a class="el" href="classOpenMS_1_1String.html">String</a> path, <a class="el" href="classOpenMS_1_1String.html">String</a> precursor_path=&quot;&quot;)</td></tr>
 
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<tr class="separator:acb2e29dc60d50478abfdf1c85de60b37"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<tr class="memitem:af24d8073d250328ea7b8b7fcd66258c1"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PrecursorIonSelection.html#af24d8073d250328ea7b8b7fcd66258c1">shiftDown_</a> (<a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a>&lt;&gt; &amp;features, <a class="el" href="classOpenMS_1_1PrecursorIonSelectionPreprocessing.html">PrecursorIonSelectionPreprocessing</a> &amp;preprocessed_db, <a class="el" href="classOpenMS_1_1String.html">String</a> protein_acc)</td></tr>
 
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<tr class="separator:af24d8073d250328ea7b8b7fcd66258c1"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<tr class="memitem:a624fa4337b310adc1d7b5a2cd046284b"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PrecursorIonSelection.html#a624fa4337b310adc1d7b5a2cd046284b">shiftUp_</a> (<a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a>&lt;&gt; &amp;features, <a class="el" href="classOpenMS_1_1PrecursorIonSelectionPreprocessing.html">PrecursorIonSelectionPreprocessing</a> &amp;preprocessed_db, <a class="el" href="classOpenMS_1_1String.html">String</a> protein_acc)</td></tr>
 
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<tr class="separator:a624fa4337b310adc1d7b5a2cd046284b"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<tr class="memitem:aaf258e1a9846d9b238ee4b3005ad3ee9"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PrecursorIonSelection.html#aaf258e1a9846d9b238ee4b3005ad3ee9">updateMembers_</a> ()</td></tr>
 
156
<tr class="memdesc:aaf258e1a9846d9b238ee4b3005ad3ee9"><td class="mdescLeft">&#160;</td><td class="mdescRight">update members method from <a class="el" href="classOpenMS_1_1DefaultParamHandler.html" title="A base class for all classes handling default parameters. ">DefaultParamHandler</a> to update the members  <a href="#aaf258e1a9846d9b238ee4b3005ad3ee9">More...</a><br/></td></tr>
 
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<tr class="separator:aaf258e1a9846d9b238ee4b3005ad3ee9"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<tr class="memitem:a75c7dfe3f9c66bb88cddfa8114f4bf3a"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PrecursorIonSelection.html#a75c7dfe3f9c66bb88cddfa8114f4bf3a">rescore_</a> (<a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a>&lt;&gt; &amp;features, std::vector&lt; <a class="el" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> &gt; &amp;new_pep_ids, <a class="el" href="classOpenMS_1_1PrecursorIonSelectionPreprocessing.html">PrecursorIonSelectionPreprocessing</a> &amp;preprocessed_db, <a class="el" href="classOpenMS_1_1PSProteinInference.html">PSProteinInference</a> &amp;protein_inference)</td></tr>
 
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<tr class="separator:a75c7dfe3f9c66bb88cddfa8114f4bf3a"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<tr class="memitem:a0ba2af27eed4a20a90c2bcbf38fb99c2"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PrecursorIonSelection.html#a0ba2af27eed4a20a90c2bcbf38fb99c2">checkForRequiredUserParams_</a> (<a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a>&lt;&gt; &amp;features)</td></tr>
 
161
<tr class="memdesc:a0ba2af27eed4a20a90c2bcbf38fb99c2"><td class="mdescLeft">&#160;</td><td class="mdescRight">Adds user params, required for the use of IPS, to a feature map using default values.  <a href="#a0ba2af27eed4a20a90c2bcbf38fb99c2">More...</a><br/></td></tr>
 
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<tr class="separator:a0ba2af27eed4a20a90c2bcbf38fb99c2"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<tr class="memitem:a85129a27fe26219e1355af4bd137a948"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PrecursorIonSelection.html#a85129a27fe26219e1355af4bd137a948">filterProtIds_</a> (std::vector&lt; <a class="el" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a> &gt; &amp;prot_ids)</td></tr>
 
164
<tr class="memdesc:a85129a27fe26219e1355af4bd137a948"><td class="mdescLeft">&#160;</td><td class="mdescRight">Groups protein identifications that cannot be distinguished by their peptide identifications.  <a href="#a85129a27fe26219e1355af4bd137a948">More...</a><br/></td></tr>
 
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<tr class="separator:a85129a27fe26219e1355af4bd137a948"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<tr class="memitem:a7d4d61690457ee5edc68304c309678f7"><td class="memItemLeft" align="right" valign="top">std::vector<br class="typebreak"/>
 
167
&lt; <a class="el" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PrecursorIonSelection.html#a7d4d61690457ee5edc68304c309678f7">filterPeptideIds_</a> (std::vector&lt; <a class="el" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> &gt; &amp;pep_ids)</td></tr>
 
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<tr class="separator:a7d4d61690457ee5edc68304c309678f7"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
169
<tr class="memitem:a2499e2cd822d59dc3f8edbc339b043b3"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PrecursorIonSelection.html#a2499e2cd822d59dc3f8edbc339b043b3">convertPeptideIdScores_</a> (std::vector&lt; <a class="el" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> &gt; &amp;pep_ids)</td></tr>
 
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<tr class="separator:a2499e2cd822d59dc3f8edbc339b043b3"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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</table><table class="memberdecls">
 
172
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pri-attribs"></a>
 
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Private Attributes</h2></td></tr>
 
174
<tr class="memitem:a1d33655f6c9055337571b352a0f8c688"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PrecursorIonSelection.html#a1d33655f6c9055337571b352a0f8c688">min_pep_ids_</a></td></tr>
 
175
<tr class="memdesc:a1d33655f6c9055337571b352a0f8c688"><td class="mdescLeft">&#160;</td><td class="mdescRight">minimal number of peptides identified for a protein to be declared identified  <a href="#a1d33655f6c9055337571b352a0f8c688">More...</a><br/></td></tr>
 
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<tr class="separator:a1d33655f6c9055337571b352a0f8c688"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<tr class="memitem:a350439a140c1f53c49e6a414063bec95"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PrecursorIonSelection.html#a350439a140c1f53c49e6a414063bec95">max_score_</a></td></tr>
 
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<tr class="memdesc:a350439a140c1f53c49e6a414063bec95"><td class="mdescLeft">&#160;</td><td class="mdescRight">maximal score in the <a class="el" href="classOpenMS_1_1FeatureMap.html" title="A container for features. ">FeatureMap</a>  <a href="#a350439a140c1f53c49e6a414063bec95">More...</a><br/></td></tr>
 
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<tr class="separator:a350439a140c1f53c49e6a414063bec95"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<tr class="memitem:ae96b07c06ceff094f476fd92cbe89e10"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1PrecursorIonSelection.html#a1d1cfd8ffb84e947f82999c682b666a7">Type</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PrecursorIonSelection.html#ae96b07c06ceff094f476fd92cbe89e10">type_</a></td></tr>
 
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<tr class="memdesc:ae96b07c06ceff094f476fd92cbe89e10"><td class="mdescLeft">&#160;</td><td class="mdescRight">precursor ion selection strategy  <a href="#ae96b07c06ceff094f476fd92cbe89e10">More...</a><br/></td></tr>
 
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<tr class="separator:ae96b07c06ceff094f476fd92cbe89e10"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<tr class="memitem:ae7c765448d55eedc24f212e92602a8ec"><td class="memItemLeft" align="right" valign="top">std::map&lt; <a class="el" href="classOpenMS_1_1String.html">String</a>, std::set<br class="typebreak"/>
 
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&lt; <a class="el" href="classOpenMS_1_1String.html">String</a> &gt; &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PrecursorIonSelection.html#ae7c765448d55eedc24f212e92602a8ec">prot_id_counter_</a></td></tr>
 
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<tr class="memdesc:ae7c765448d55eedc24f212e92602a8ec"><td class="mdescLeft">&#160;</td><td class="mdescRight">stores the peptide sequences for all protein identifications  <a href="#ae7c765448d55eedc24f212e92602a8ec">More...</a><br/></td></tr>
 
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<tr class="separator:ae7c765448d55eedc24f212e92602a8ec"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<tr class="memitem:a0d138c04b4994b24723c3d3fc7d76209"><td class="memItemLeft" align="right" valign="top">std::vector&lt; <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PrecursorIonSelection.html#a0d138c04b4994b24723c3d3fc7d76209">fraction_counter_</a></td></tr>
 
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<tr class="memdesc:a0d138c04b4994b24723c3d3fc7d76209"><td class="mdescLeft">&#160;</td><td class="mdescRight">stores the number of selected precursors per fraction  <a href="#a0d138c04b4994b24723c3d3fc7d76209">More...</a><br/></td></tr>
 
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<tr class="separator:a0d138c04b4994b24723c3d3fc7d76209"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<tr class="memitem:aa0d44a6be23374eb5d1f099ef8b4ca82"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PrecursorIonSelection.html#aa0d44a6be23374eb5d1f099ef8b4ca82">mz_tolerance_</a></td></tr>
 
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<tr class="memdesc:aa0d44a6be23374eb5d1f099ef8b4ca82"><td class="mdescLeft">&#160;</td><td class="mdescRight">precursor ion error tolerance  <a href="#aa0d44a6be23374eb5d1f099ef8b4ca82">More...</a><br/></td></tr>
 
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<tr class="separator:aa0d44a6be23374eb5d1f099ef8b4ca82"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<tr class="memitem:a05ce08b9b0435cc41cb9f2528c313237"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1String.html">String</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PrecursorIonSelection.html#a05ce08b9b0435cc41cb9f2528c313237">mz_tolerance_unit_</a></td></tr>
 
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<tr class="memdesc:a05ce08b9b0435cc41cb9f2528c313237"><td class="mdescLeft">&#160;</td><td class="mdescRight">precursor ion error tolerance unit (ppm or Da)  <a href="#a05ce08b9b0435cc41cb9f2528c313237">More...</a><br/></td></tr>
 
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<tr class="separator:a05ce08b9b0435cc41cb9f2528c313237"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<tr class="memitem:a78c0d505b8706df48e8cf696e21035ee"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PrecursorIonSelection.html#a78c0d505b8706df48e8cf696e21035ee">max_iteration_</a></td></tr>
 
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<tr class="memdesc:a78c0d505b8706df48e8cf696e21035ee"><td class="mdescLeft">&#160;</td><td class="mdescRight">maximal number of iterations  <a href="#a78c0d505b8706df48e8cf696e21035ee">More...</a><br/></td></tr>
 
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<tr class="separator:a78c0d505b8706df48e8cf696e21035ee"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<tr class="memitem:a3ff6e92379e0c12cecff4f086c60b0b7"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PrecursorIonSelection.html#a3ff6e92379e0c12cecff4f086c60b0b7">x_variable_number_</a></td></tr>
 
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<tr class="separator:a3ff6e92379e0c12cecff4f086c60b0b7"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<tr class="memitem:afb8f1202d548f01394d85fbeb51f9adf"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1LPWrapper.html#ab659f8690ca779b8c3d73fe524a39a00">LPWrapper::SOLVER</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PrecursorIonSelection.html#afb8f1202d548f01394d85fbeb51f9adf">solver_</a></td></tr>
 
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<tr class="separator:afb8f1202d548f01394d85fbeb51f9adf"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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</table><table class="memberdecls">
 
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="inherited"></a>
 
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Additional Inherited Members</h2></td></tr>
 
206
<tr class="inherit_header pro_methods_classOpenMS_1_1DefaultParamHandler"><td colspan="2" onclick="javascript:toggleInherit('pro_methods_classOpenMS_1_1DefaultParamHandler')"><img src="closed.png" alt="-"/>&#160;Protected Member Functions inherited from <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td></tr>
 
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<tr class="memitem:a2802c591e6d7fd3fd9cc35f5e875d0ba inherit pro_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a2802c591e6d7fd3fd9cc35f5e875d0ba">defaultsToParam_</a> ()</td></tr>
 
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<tr class="memdesc:a2802c591e6d7fd3fd9cc35f5e875d0ba inherit pro_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft">&#160;</td><td class="mdescRight">Updates the parameters after the defaults have been set in the constructor.  <a href="#a2802c591e6d7fd3fd9cc35f5e875d0ba">More...</a><br/></td></tr>
 
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<tr class="separator:a2802c591e6d7fd3fd9cc35f5e875d0ba inherit pro_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<tr class="inherit_header pro_attribs_classOpenMS_1_1DefaultParamHandler"><td colspan="2" onclick="javascript:toggleInherit('pro_attribs_classOpenMS_1_1DefaultParamHandler')"><img src="closed.png" alt="-"/>&#160;Protected Attributes inherited from <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td></tr>
 
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<tr class="memitem:a28c73e623c63a4fe3bfceb1ae8274f39 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1Param.html">Param</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a></td></tr>
 
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<tr class="memdesc:a28c73e623c63a4fe3bfceb1ae8274f39 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft">&#160;</td><td class="mdescRight">Container for current parameters.  <a href="#a28c73e623c63a4fe3bfceb1ae8274f39">More...</a><br/></td></tr>
 
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<tr class="separator:a28c73e623c63a4fe3bfceb1ae8274f39 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<tr class="memitem:a761b1937850c141d0c6fff0e4d633a04 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1Param.html">Param</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a></td></tr>
 
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<tr class="memdesc:a761b1937850c141d0c6fff0e4d633a04 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft">&#160;</td><td class="mdescRight">Container for default parameters. This member should be filled in the constructor of derived classes!  <a href="#a761b1937850c141d0c6fff0e4d633a04">More...</a><br/></td></tr>
 
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<tr class="separator:a761b1937850c141d0c6fff0e4d633a04 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<tr class="memitem:ac4b0e20bc59c7a5afe016c69067e428c inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">std::vector&lt; <a class="el" href="classOpenMS_1_1String.html">String</a> &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#ac4b0e20bc59c7a5afe016c69067e428c">subsections_</a></td></tr>
 
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<tr class="memdesc:ac4b0e20bc59c7a5afe016c69067e428c inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft">&#160;</td><td class="mdescRight">Container for registered subsections. This member should be filled in the constructor of derived classes!  <a href="#ac4b0e20bc59c7a5afe016c69067e428c">More...</a><br/></td></tr>
 
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<tr class="separator:ac4b0e20bc59c7a5afe016c69067e428c inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<tr class="memitem:a5a51f3f150b09068256195e934339a19 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1String.html">String</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a5a51f3f150b09068256195e934339a19">error_name_</a></td></tr>
 
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<tr class="memdesc:a5a51f3f150b09068256195e934339a19 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft">&#160;</td><td class="mdescRight">Name that is displayed in error messages during the parameter checking.  <a href="#a5a51f3f150b09068256195e934339a19">More...</a><br/></td></tr>
 
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<tr class="separator:a5a51f3f150b09068256195e934339a19 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<tr class="memitem:a7c3b265b697a57615da5cd3274780efd inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a7c3b265b697a57615da5cd3274780efd">check_defaults_</a></td></tr>
 
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<tr class="memdesc:a7c3b265b697a57615da5cd3274780efd inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft">&#160;</td><td class="mdescRight">If this member is set to false no checking if parameters in done;.  <a href="#a7c3b265b697a57615da5cd3274780efd">More...</a><br/></td></tr>
 
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<tr class="separator:a7c3b265b697a57615da5cd3274780efd inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<tr class="memitem:aba444910e4fccb93f91bf7ab135f508a inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#aba444910e4fccb93f91bf7ab135f508a">warn_empty_defaults_</a></td></tr>
 
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<tr class="memdesc:aba444910e4fccb93f91bf7ab135f508a inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft">&#160;</td><td class="mdescRight">If this member is set to false no warning is emitted when defaults are empty;.  <a href="#aba444910e4fccb93f91bf7ab135f508a">More...</a><br/></td></tr>
 
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<tr class="separator:aba444910e4fccb93f91bf7ab135f508a inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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</table>
 
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<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
 
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<div class="textblock"><p>This class implements different precursor ion selection strategies. </p>
 
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<B>Parameters of this class are:</B><BR><BR>
 
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<table border="1" style="border-style:solid; border-collapse:collapse; border-color:#c0c0c0;" width="100%" cellpadding="4">
 
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<tr style="border-bottom:1px solid black; background:#fffff0"><th>Name</th><th>Type</th><th>Default</th><th>Restrictions</th><th>Description</th></tr>
 
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<tr>
 
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  <td style="vertical-align:top"><b>type</b></td>
 
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  <td style="vertical-align:top">string</td><td style="vertical-align:top">IPS</td>
 
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  <td style="vertical-align:top">ILP_IPS, IPS, SPS, Upshift, Downshift, DEX</td><td style="vertical-align:top">Strategy for precursor ion selection.</td>
 
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</tr>
 
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<tr>
 
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  <td style="vertical-align:top"><b>max_iteration</b></td>
 
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  <td style="vertical-align:top">int</td><td style="vertical-align:top">100</td>
 
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  <td style="vertical-align:top">min: 1</td><td style="vertical-align:top">Maximal number of iterations.</td>
 
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</tr>
 
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<tr>
 
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  <td style="vertical-align:top"><b>rt_bin_capacity</b></td>
 
247
  <td style="vertical-align:top">int</td><td style="vertical-align:top">10</td>
 
248
  <td style="vertical-align:top">min: 1</td><td style="vertical-align:top">Maximal number of precursors per rt bin.</td>
 
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</tr>
 
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<tr>
 
251
  <td style="vertical-align:top"><b>step_size</b></td>
 
252
  <td style="vertical-align:top">int</td><td style="vertical-align:top">1</td>
 
253
  <td style="vertical-align:top">min: 1</td><td style="vertical-align:top">Maximal number of precursors per iteration.</td>
 
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</tr>
 
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<tr>
 
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  <td style="vertical-align:top"><b>peptide_min_prob</b></td>
 
257
  <td style="vertical-align:top">float</td><td style="vertical-align:top">0.2</td>
 
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  <td style="vertical-align:top">&nbsp;</td><td style="vertical-align:top">Minimal peptide probability.</td>
 
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</tr>
 
260
<tr>
 
261
  <td style="vertical-align:top"><b>sequential_spectrum_order</b></td>
 
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  <td style="vertical-align:top">string</td><td style="vertical-align:top">false</td>
 
263
  <td style="vertical-align:top">true, false</td><td style="vertical-align:top">If true, precursors are selected sequentially with respect to their RT.</td>
 
264
</tr>
 
265
<tr>
 
266
  <td style="vertical-align:top"><b>MIPFormulation:thresholds:min_protein_probability</b></td>
 
267
  <td style="vertical-align:top">float</td><td style="vertical-align:top">0.2</td>
 
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  <td style="vertical-align:top">min: 0 max: 1</td><td style="vertical-align:top">Minimal protein probability for a protein to be considered in the ILP</td>
 
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</tr>
 
270
<tr>
 
271
  <td style="vertical-align:top"><b>MIPFormulation:thresholds:min_protein_id_probability</b></td>
 
272
  <td style="vertical-align:top">float</td><td style="vertical-align:top">0.95</td>
 
273
  <td style="vertical-align:top">min: 0 max: 1</td><td style="vertical-align:top">Minimal protein probability for a protein to be considered identified.</td>
 
274
</tr>
 
275
<tr>
 
276
  <td style="vertical-align:top"><b>MIPFormulation:thresholds:min_pt_weight</b></td>
 
277
  <td style="vertical-align:top">float</td><td style="vertical-align:top">0.5</td>
 
278
  <td style="vertical-align:top">min: 0 max: 1</td><td style="vertical-align:top">Minimal pt weight of a precursor</td>
 
279
</tr>
 
280
<tr>
 
281
  <td style="vertical-align:top"><b>MIPFormulation:thresholds:min_mz</b></td>
 
282
  <td style="vertical-align:top">float</td><td style="vertical-align:top">500</td>
 
283
  <td style="vertical-align:top">min: 0</td><td style="vertical-align:top">Minimal mz to be considered in protein based LP formulation.</td>
 
284
</tr>
 
285
<tr>
 
286
  <td style="vertical-align:top"><b>MIPFormulation:thresholds:max_mz</b></td>
 
287
  <td style="vertical-align:top">float</td><td style="vertical-align:top">5000</td>
 
288
  <td style="vertical-align:top">min: 0</td><td style="vertical-align:top">Minimal mz to be considered in protein based LP formulation.</td>
 
289
</tr>
 
290
<tr>
 
291
  <td style="vertical-align:top"><b>MIPFormulation:thresholds:min_pred_pep_prob</b></td>
 
292
  <td style="vertical-align:top">float</td><td style="vertical-align:top">0.5</td>
 
293
  <td style="vertical-align:top">min: 0 max: 1</td><td style="vertical-align:top">Minimal predicted peptide probability of a precursor</td>
 
294
</tr>
 
295
<tr>
 
296
  <td style="vertical-align:top"><b>MIPFormulation:thresholds:min_rt_weight</b></td>
 
297
  <td style="vertical-align:top">float</td><td style="vertical-align:top">0.5</td>
 
298
  <td style="vertical-align:top">min: 0 max: 1</td><td style="vertical-align:top">Minimal rt weight of a precursor</td>
 
299
</tr>
 
300
<tr>
 
301
  <td style="vertical-align:top"><b>MIPFormulation:thresholds:use_peptide_rule</b></td>
 
302
  <td style="vertical-align:top">string</td><td style="vertical-align:top">false</td>
 
303
  <td style="vertical-align:top">true, false</td><td style="vertical-align:top">Use peptide rule instead of minimal protein id probability</td>
 
304
</tr>
 
305
<tr>
 
306
  <td style="vertical-align:top"><b>MIPFormulation:thresholds:min_peptide_ids</b></td>
 
307
  <td style="vertical-align:top">int</td><td style="vertical-align:top">2</td>
 
308
  <td style="vertical-align:top">min: 1</td><td style="vertical-align:top">If use_peptide_rule is true, this parameter sets the minimal number of peptide ids for a protein id</td>
 
309
</tr>
 
310
<tr>
 
311
  <td style="vertical-align:top"><b>MIPFormulation:thresholds:min_peptide_probability</b></td>
 
312
  <td style="vertical-align:top">float</td><td style="vertical-align:top">0.95</td>
 
313
  <td style="vertical-align:top">min: 0 max: 1</td><td style="vertical-align:top">If use_peptide_rule is true, this parameter sets the minimal probability for a peptide to be safely identified</td>
 
314
</tr>
 
315
<tr>
 
316
  <td style="vertical-align:top"><b>MIPFormulation:combined_ilp:k1</b></td>
 
317
  <td style="vertical-align:top">float</td><td style="vertical-align:top">0.2</td>
 
318
  <td style="vertical-align:top">min: 0</td><td style="vertical-align:top">combined ilp: weight for z_i</td>
 
319
</tr>
 
320
<tr>
 
321
  <td style="vertical-align:top"><b>MIPFormulation:combined_ilp:k2</b></td>
 
322
  <td style="vertical-align:top">float</td><td style="vertical-align:top">0.2</td>
 
323
  <td style="vertical-align:top">min: 0</td><td style="vertical-align:top">combined ilp: weight for x_j,s*int_j,s</td>
 
324
</tr>
 
325
<tr>
 
326
  <td style="vertical-align:top"><b>MIPFormulation:combined_ilp:k3</b></td>
 
327
  <td style="vertical-align:top">float</td><td style="vertical-align:top">0.4</td>
 
328
  <td style="vertical-align:top">min: 0</td><td style="vertical-align:top">combined ilp: weight for -x_j,s*w_j,s</td>
 
329
</tr>
 
330
<tr>
 
331
  <td style="vertical-align:top"><b>MIPFormulation:combined_ilp:scale_matching_probs</b></td>
 
332
  <td style="vertical-align:top">string</td><td style="vertical-align:top">true</td>
 
333
  <td style="vertical-align:top">true, false</td><td style="vertical-align:top">flag if detectability * rt_weight shall be scaled to cover all [0,1]</td>
 
334
</tr>
 
335
<tr>
 
336
  <td style="vertical-align:top"><b>Preprocessing:precursor_mass_tolerance</b></td>
 
337
  <td style="vertical-align:top">float</td><td style="vertical-align:top">10</td>
 
338
  <td style="vertical-align:top">min: 0</td><td style="vertical-align:top">Precursor mass tolerance which is used to query the peptide database for peptides</td>
 
339
</tr>
 
340
<tr>
 
341
  <td style="vertical-align:top"><b>Preprocessing:precursor_mass_tolerance_unit</b></td>
 
342
  <td style="vertical-align:top">string</td><td style="vertical-align:top">ppm</td>
 
343
  <td style="vertical-align:top">ppm, Da</td><td style="vertical-align:top">Precursor mass tolerance unit.</td>
 
344
</tr>
 
345
<tr>
 
346
  <td style="vertical-align:top"><b>Preprocessing:preprocessed_db_path</b></td>
 
347
  <td style="vertical-align:top">string</td><td style="vertical-align:top"></td>
 
348
  <td style="vertical-align:top">&nbsp;</td><td style="vertical-align:top">Path where the preprocessed database should be stored</td>
 
349
</tr>
 
350
<tr>
 
351
  <td style="vertical-align:top"><b>Preprocessing:preprocessed_db_pred_rt_path</b></td>
 
352
  <td style="vertical-align:top">string</td><td style="vertical-align:top"></td>
 
353
  <td style="vertical-align:top">&nbsp;</td><td style="vertical-align:top">Path where the predicted rts of the preprocessed database should be stored</td>
 
354
</tr>
 
355
<tr>
 
356
  <td style="vertical-align:top"><b>Preprocessing:preprocessed_db_pred_dt_path</b></td>
 
357
  <td style="vertical-align:top">string</td><td style="vertical-align:top"></td>
 
358
  <td style="vertical-align:top">&nbsp;</td><td style="vertical-align:top">Path where the predicted rts of the preprocessed database should be stored</td>
 
359
</tr>
 
360
<tr>
 
361
  <td style="vertical-align:top"><b>Preprocessing:max_peptides_per_run</b></td>
 
362
  <td style="vertical-align:top">int</td><td style="vertical-align:top">100000</td>
 
363
  <td style="vertical-align:top">min: 1</td><td style="vertical-align:top">Number of peptides for that the pt and rt are parallely predicted.</td>
 
364
</tr>
 
365
<tr>
 
366
  <td style="vertical-align:top"><b>Preprocessing:missed_cleavages</b></td>
 
367
  <td style="vertical-align:top">int</td><td style="vertical-align:top">1</td>
 
368
  <td style="vertical-align:top">min: 0</td><td style="vertical-align:top">Number of allowed missed cleavages.</td>
 
369
</tr>
 
370
<tr>
 
371
  <td style="vertical-align:top"><b>Preprocessing:taxonomy</b></td>
 
372
  <td style="vertical-align:top">string</td><td style="vertical-align:top"></td>
 
373
  <td style="vertical-align:top">&nbsp;</td><td style="vertical-align:top">Taxonomy</td>
 
374
</tr>
 
375
<tr>
 
376
  <td style="vertical-align:top"><b>Preprocessing:tmp_dir</b></td>
 
377
  <td style="vertical-align:top">string</td><td style="vertical-align:top"></td>
 
378
  <td style="vertical-align:top">&nbsp;</td><td style="vertical-align:top">Absolute path to tmp data directory used to store files needed for rt and dt prediction.</td>
 
379
</tr>
 
380
<tr>
 
381
  <td style="vertical-align:top"><b>Preprocessing:store_peptide_sequences</b></td>
 
382
  <td style="vertical-align:top">string</td><td style="vertical-align:top">false</td>
 
383
  <td style="vertical-align:top">&nbsp;</td><td style="vertical-align:top">Flag if peptide sequences should be stored.</td>
 
384
</tr>
 
385
<tr>
 
386
  <td style="vertical-align:top"><b>Preprocessing:rt_settings:min_rt</b></td>
 
387
  <td style="vertical-align:top">float</td><td style="vertical-align:top">960</td>
 
388
  <td style="vertical-align:top">min: 1</td><td style="vertical-align:top">Minimal RT in the experiment (in seconds)</td>
 
389
</tr>
 
390
<tr>
 
391
  <td style="vertical-align:top"><b>Preprocessing:rt_settings:max_rt</b></td>
 
392
  <td style="vertical-align:top">float</td><td style="vertical-align:top">3840</td>
 
393
  <td style="vertical-align:top">&nbsp;</td><td style="vertical-align:top">Maximal RT in the experiment (in seconds)</td>
 
394
</tr>
 
395
<tr>
 
396
  <td style="vertical-align:top"><b>Preprocessing:rt_settings:rt_step_size</b></td>
 
397
  <td style="vertical-align:top">float</td><td style="vertical-align:top">30</td>
 
398
  <td style="vertical-align:top">&nbsp;</td><td style="vertical-align:top">Time between two consecutive spectra (in seconds)</td>
 
399
</tr>
 
400
<tr>
 
401
  <td style="vertical-align:top"><b>Preprocessing:rt_settings:gauss_mean</b></td>
 
402
  <td style="vertical-align:top">float</td><td style="vertical-align:top">-1</td>
 
403
  <td style="vertical-align:top">&nbsp;</td><td style="vertical-align:top">mean of the gauss curve</td>
 
404
</tr>
 
405
<tr>
 
406
  <td style="vertical-align:top"><b>Preprocessing:rt_settings:gauss_sigma</b></td>
 
407
  <td style="vertical-align:top">float</td><td style="vertical-align:top">3</td>
 
408
  <td style="vertical-align:top">&nbsp;</td><td style="vertical-align:top">std of the gauss curve</td>
 
409
</tr>
 
410
</table>
 
411
<br>
 
412
<b>Note:</b>
 
413
<UL style="margin-top:0px;">
 
414
  <LI> If a section name is documented, the documentation is displayed as tooltip.
 
415
  <LI> Advanced parameter names are italic.
 
416
</UL>
 
417
 </div><h2 class="groupheader">Member Enumeration Documentation</h2>
 
418
<a class="anchor" id="a1d1cfd8ffb84e947f82999c682b666a7"></a>
 
419
<div class="memitem">
 
420
<div class="memproto">
 
421
      <table class="memname">
 
422
        <tr>
 
423
          <td class="memname">enum <a class="el" href="classOpenMS_1_1PrecursorIonSelection.html#a1d1cfd8ffb84e947f82999c682b666a7">Type</a></td>
 
424
        </tr>
 
425
      </table>
 
426
</div><div class="memdoc">
 
427
 
 
428
<p><a class="el" href="classOpenMS_1_1Precursor.html" title="Precursor meta information. ">Precursor</a> ion selection type (iterative, static, upshift, downshift, dynamic exclusion). </p>
 
429
<p>The iterative strategy changes the ranking of possible precursors based on identification results from previous iterations.</p>
 
430
<p>The upshift strategy assigns a higher priority to precursors whose masses are matching peptide masses of potential protein identifications to enable a safe identification in the next iterations.</p>
 
431
<p>The downshift strategy assigns a lower priority to precursors whose masses are matching peptide masses of safe protein identifications.</p>
 
432
<p>The dynamic exclusion exludes precursors whose masses are matching peptide masses of safe protein identifications.</p>
 
433
<p>The static selection uses precomputed scores to rank the precursor, the order of precursors isn't changed throughout the run. </p>
 
434
<table class="fieldtable">
 
435
<tr><th colspan="2">Enumerator</th></tr><tr><td class="fieldname"><em><a class="anchor" id="a1d1cfd8ffb84e947f82999c682b666a7aafb6828f5a8b8b40648e96ce2e5f435b"></a>IPS</em>&nbsp;</td><td class="fielddoc">
 
436
</td></tr>
 
437
<tr><td class="fieldname"><em><a class="anchor" id="a1d1cfd8ffb84e947f82999c682b666a7a241370a8eee3fc0070dce7c2cc8da0b6"></a>ILP_IPS</em>&nbsp;</td><td class="fielddoc">
 
438
</td></tr>
 
439
<tr><td class="fieldname"><em><a class="anchor" id="a1d1cfd8ffb84e947f82999c682b666a7a38aefbb94f63c43b1c8047151c83ca64"></a>SPS</em>&nbsp;</td><td class="fielddoc">
 
440
</td></tr>
 
441
<tr><td class="fieldname"><em><a class="anchor" id="a1d1cfd8ffb84e947f82999c682b666a7aa58d945ae9279992a5a9a1e908b770cb"></a>UPSHIFT</em>&nbsp;</td><td class="fielddoc">
 
442
</td></tr>
 
443
<tr><td class="fieldname"><em><a class="anchor" id="a1d1cfd8ffb84e947f82999c682b666a7a3ad159e1881c0b9db5274d155c9faf28"></a>DOWNSHIFT</em>&nbsp;</td><td class="fielddoc">
 
444
</td></tr>
 
445
<tr><td class="fieldname"><em><a class="anchor" id="a1d1cfd8ffb84e947f82999c682b666a7afd8b47cd00ea3ad6c3c275e1ffcce606"></a>DEX</em>&nbsp;</td><td class="fielddoc">
 
446
</td></tr>
 
447
</table>
 
448
 
 
449
</div>
 
450
</div>
 
451
<h2 class="groupheader">Constructor &amp; Destructor Documentation</h2>
 
452
<a class="anchor" id="ac48bbb4aaf4fb10469d05f954810c67d"></a>
 
453
<div class="memitem">
 
454
<div class="memproto">
 
455
      <table class="memname">
 
456
        <tr>
 
457
          <td class="memname"><a class="el" href="classOpenMS_1_1PrecursorIonSelection.html">PrecursorIonSelection</a> </td>
 
458
          <td>(</td>
 
459
          <td class="paramname"></td><td>)</td>
 
460
          <td></td>
 
461
        </tr>
 
462
      </table>
 
463
</div><div class="memdoc">
 
464
 
 
465
</div>
 
466
</div>
 
467
<a class="anchor" id="a2d3d5a0fafc2571f619b2feb66505b2c"></a>
 
468
<div class="memitem">
 
469
<div class="memproto">
 
470
      <table class="memname">
 
471
        <tr>
 
472
          <td class="memname"><a class="el" href="classOpenMS_1_1PrecursorIonSelection.html">PrecursorIonSelection</a> </td>
 
473
          <td>(</td>
 
474
          <td class="paramtype">const <a class="el" href="classOpenMS_1_1PrecursorIonSelection.html">PrecursorIonSelection</a> &amp;&#160;</td>
 
475
          <td class="paramname"><em>source</em></td><td>)</td>
 
476
          <td></td>
 
477
        </tr>
 
478
      </table>
 
479
</div><div class="memdoc">
 
480
 
 
481
</div>
 
482
</div>
 
483
<a class="anchor" id="a339727faeacb33d458239e23e6f38a5c"></a>
 
484
<div class="memitem">
 
485
<div class="memproto">
 
486
      <table class="memname">
 
487
        <tr>
 
488
          <td class="memname">~<a class="el" href="classOpenMS_1_1PrecursorIonSelection.html">PrecursorIonSelection</a> </td>
 
489
          <td>(</td>
 
490
          <td class="paramname"></td><td>)</td>
 
491
          <td></td>
 
492
        </tr>
 
493
      </table>
 
494
</div><div class="memdoc">
 
495
 
 
496
</div>
 
497
</div>
 
498
<h2 class="groupheader">Member Function Documentation</h2>
 
499
<a class="anchor" id="a0ba2af27eed4a20a90c2bcbf38fb99c2"></a>
 
500
<div class="memitem">
 
501
<div class="memproto">
 
502
<table class="mlabels">
 
503
  <tr>
 
504
  <td class="mlabels-left">
 
505
      <table class="memname">
 
506
        <tr>
 
507
          <td class="memname">void checkForRequiredUserParams_ </td>
 
508
          <td>(</td>
 
509
          <td class="paramtype"><a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a>&lt;&gt; &amp;&#160;</td>
 
510
          <td class="paramname"><em>features</em></td><td>)</td>
 
511
          <td></td>
 
512
        </tr>
 
513
      </table>
 
514
  </td>
 
515
  <td class="mlabels-right">
 
516
<span class="mlabels"><span class="mlabel">private</span></span>  </td>
 
517
  </tr>
 
518
</table>
 
519
</div><div class="memdoc">
 
520
 
 
521
<p>Adds user params, required for the use of IPS, to a feature map using default values. </p>
 
522
<dl class="params"><dt>Parameters</dt><dd>
 
523
  <table class="params">
 
524
    <tr><td class="paramname">features</td><td><a class="el" href="classOpenMS_1_1FeatureMap.html" title="A container for features. ">FeatureMap</a> with all possible precursors </td></tr>
 
525
  </table>
 
526
  </dd>
 
527
</dl>
 
528
 
 
529
</div>
 
530
</div>
 
531
<a class="anchor" id="a2499e2cd822d59dc3f8edbc339b043b3"></a>
 
532
<div class="memitem">
 
533
<div class="memproto">
 
534
<table class="mlabels">
 
535
  <tr>
 
536
  <td class="mlabels-left">
 
537
      <table class="memname">
 
538
        <tr>
 
539
          <td class="memname">void convertPeptideIdScores_ </td>
 
540
          <td>(</td>
 
541
          <td class="paramtype">std::vector&lt; <a class="el" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> &gt; &amp;&#160;</td>
 
542
          <td class="paramname"><em>pep_ids</em></td><td>)</td>
 
543
          <td></td>
 
544
        </tr>
 
545
      </table>
 
546
  </td>
 
547
  <td class="mlabels-right">
 
548
<span class="mlabels"><span class="mlabel">private</span></span>  </td>
 
549
  </tr>
 
550
</table>
 
551
</div><div class="memdoc">
 
552
 
 
553
</div>
 
554
</div>
 
555
<a class="anchor" id="a7d4d61690457ee5edc68304c309678f7"></a>
 
556
<div class="memitem">
 
557
<div class="memproto">
 
558
<table class="mlabels">
 
559
  <tr>
 
560
  <td class="mlabels-left">
 
561
      <table class="memname">
 
562
        <tr>
 
563
          <td class="memname">std::vector&lt;<a class="el" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a>&gt; filterPeptideIds_ </td>
 
564
          <td>(</td>
 
565
          <td class="paramtype">std::vector&lt; <a class="el" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> &gt; &amp;&#160;</td>
 
566
          <td class="paramname"><em>pep_ids</em></td><td>)</td>
 
567
          <td></td>
 
568
        </tr>
 
569
      </table>
 
570
  </td>
 
571
  <td class="mlabels-right">
 
572
<span class="mlabels"><span class="mlabel">private</span></span>  </td>
 
573
  </tr>
 
574
</table>
 
575
</div><div class="memdoc">
 
576
 
 
577
</div>
 
578
</div>
 
579
<a class="anchor" id="a85129a27fe26219e1355af4bd137a948"></a>
 
580
<div class="memitem">
 
581
<div class="memproto">
 
582
<table class="mlabels">
 
583
  <tr>
 
584
  <td class="mlabels-left">
 
585
      <table class="memname">
 
586
        <tr>
 
587
          <td class="memname"><a class="el" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a> filterProtIds_ </td>
 
588
          <td>(</td>
 
589
          <td class="paramtype">std::vector&lt; <a class="el" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a> &gt; &amp;&#160;</td>
 
590
          <td class="paramname"><em>prot_ids</em></td><td>)</td>
 
591
          <td></td>
 
592
        </tr>
 
593
      </table>
 
594
  </td>
 
595
  <td class="mlabels-right">
 
596
<span class="mlabels"><span class="mlabel">private</span></span>  </td>
 
597
  </tr>
 
598
</table>
 
599
</div><div class="memdoc">
 
600
 
 
601
<p>Groups protein identifications that cannot be distinguished by their peptide identifications. </p>
 
602
<dl class="params"><dt>Parameters</dt><dd>
 
603
  <table class="params">
 
604
    <tr><td class="paramname">prot_ids</td><td>All protein identifications. </td></tr>
 
605
  </table>
 
606
  </dd>
 
607
</dl>
 
608
 
 
609
</div>
 
610
</div>
 
611
<a class="anchor" id="ac945a0966726a3a644d194b81c28d960"></a>
 
612
<div class="memitem">
 
613
<div class="memproto">
 
614
<table class="mlabels">
 
615
  <tr>
 
616
  <td class="mlabels-left">
 
617
      <table class="memname">
 
618
        <tr>
 
619
          <td class="memname"><a class="el" href="classOpenMS_1_1LPWrapper.html#ab659f8690ca779b8c3d73fe524a39a00">LPWrapper::SOLVER</a> getLPSolver </td>
 
620
          <td>(</td>
 
621
          <td class="paramname"></td><td>)</td>
 
622
          <td></td>
 
623
        </tr>
 
624
      </table>
 
625
  </td>
 
626
  <td class="mlabels-right">
 
627
<span class="mlabels"><span class="mlabel">inline</span></span>  </td>
 
628
  </tr>
 
629
</table>
 
630
</div><div class="memdoc">
 
631
 
 
632
</div>
 
633
</div>
 
634
<a class="anchor" id="a136d8fee61d49118a5203b54fa621ea0"></a>
 
635
<div class="memitem">
 
636
<div class="memproto">
 
637
      <table class="memname">
 
638
        <tr>
 
639
          <td class="memname">const <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a>&amp; getMaxScore </td>
 
640
          <td>(</td>
 
641
          <td class="paramname"></td><td>)</td>
 
642
          <td> const</td>
 
643
        </tr>
 
644
      </table>
 
645
</div><div class="memdoc">
 
646
 
 
647
</div>
 
648
</div>
 
649
<a class="anchor" id="acaecf1b0ad521b2841e6946d9608db7b"></a>
 
650
<div class="memitem">
 
651
<div class="memproto">
 
652
      <table class="memname">
 
653
        <tr>
 
654
          <td class="memname">void getNextPrecursors </td>
 
655
          <td>(</td>
 
656
          <td class="paramtype"><a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a>&lt;&gt; &amp;&#160;</td>
 
657
          <td class="paramname"><em>features</em>, </td>
 
658
        </tr>
 
659
        <tr>
 
660
          <td class="paramkey"></td>
 
661
          <td></td>
 
662
          <td class="paramtype"><a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a>&lt;&gt; &amp;&#160;</td>
 
663
          <td class="paramname"><em>next_features</em>, </td>
 
664
        </tr>
 
665
        <tr>
 
666
          <td class="paramkey"></td>
 
667
          <td></td>
 
668
          <td class="paramtype"><a class="el" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a>&#160;</td>
 
669
          <td class="paramname"><em>number</em>&#160;</td>
 
670
        </tr>
 
671
        <tr>
 
672
          <td></td>
 
673
          <td>)</td>
 
674
          <td></td><td></td>
 
675
        </tr>
 
676
      </table>
 
677
</div><div class="memdoc">
 
678
 
 
679
<p>Returns features with highest score for MS/MS. </p>
 
680
<dl class="params"><dt>Parameters</dt><dd>
 
681
  <table class="params">
 
682
    <tr><td class="paramname">features</td><td><a class="el" href="classOpenMS_1_1FeatureMap.html" title="A container for features. ">FeatureMap</a> with all possible precursors </td></tr>
 
683
    <tr><td class="paramname">next_features</td><td><a class="el" href="classOpenMS_1_1FeatureMap.html" title="A container for features. ">FeatureMap</a> with next precursors </td></tr>
 
684
    <tr><td class="paramname">number</td><td>Number of features to be reported </td></tr>
 
685
  </table>
 
686
  </dd>
 
687
</dl>
 
688
 
 
689
</div>
 
690
</div>
 
691
<a class="anchor" id="a1617e594e09d4f445de0ee207e13d4e1"></a>
 
692
<div class="memitem">
 
693
<div class="memproto">
 
694
      <table class="memname">
 
695
        <tr>
 
696
          <td class="memname">void getNextPrecursors </td>
 
697
          <td>(</td>
 
698
          <td class="paramtype">std::vector&lt; <a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> &gt; &amp;&#160;</td>
 
699
          <td class="paramname"><em>solution_indices</em>, </td>
 
700
        </tr>
 
701
        <tr>
 
702
          <td class="paramkey"></td>
 
703
          <td></td>
 
704
          <td class="paramtype">std::vector&lt; <a class="el" href="structOpenMS_1_1PSLPFormulation_1_1IndexTriple.html">PSLPFormulation::IndexTriple</a> &gt; &amp;&#160;</td>
 
705
          <td class="paramname"><em>variable_indices</em>, </td>
 
706
        </tr>
 
707
        <tr>
 
708
          <td class="paramkey"></td>
 
709
          <td></td>
 
710
          <td class="paramtype">std::set&lt; <a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> &gt; &amp;&#160;</td>
 
711
          <td class="paramname"><em>measured_variables</em>, </td>
 
712
        </tr>
 
713
        <tr>
 
714
          <td class="paramkey"></td>
 
715
          <td></td>
 
716
          <td class="paramtype"><a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a>&lt;&gt; &amp;&#160;</td>
 
717
          <td class="paramname"><em>features</em>, </td>
 
718
        </tr>
 
719
        <tr>
 
720
          <td class="paramkey"></td>
 
721
          <td></td>
 
722
          <td class="paramtype"><a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a>&lt;&gt; &amp;&#160;</td>
 
723
          <td class="paramname"><em>new_features</em>, </td>
 
724
        </tr>
 
725
        <tr>
 
726
          <td class="paramkey"></td>
 
727
          <td></td>
 
728
          <td class="paramtype"><a class="el" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a>&#160;</td>
 
729
          <td class="paramname"><em>step_size</em>, </td>
 
730
        </tr>
 
731
        <tr>
 
732
          <td class="paramkey"></td>
 
733
          <td></td>
 
734
          <td class="paramtype"><a class="el" href="classOpenMS_1_1PSLPFormulation.html">PSLPFormulation</a> &amp;&#160;</td>
 
735
          <td class="paramname"><em>ilp</em>&#160;</td>
 
736
        </tr>
 
737
        <tr>
 
738
          <td></td>
 
739
          <td>)</td>
 
740
          <td></td><td></td>
 
741
        </tr>
 
742
      </table>
 
743
</div><div class="memdoc">
 
744
 
 
745
</div>
 
746
</div>
 
747
<a class="anchor" id="a32956b1163d1167a2d326f2cc441de90"></a>
 
748
<div class="memitem">
 
749
<div class="memproto">
 
750
      <table class="memname">
 
751
        <tr>
 
752
          <td class="memname">void getNextPrecursorsSeq </td>
 
753
          <td>(</td>
 
754
          <td class="paramtype"><a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a>&lt;&gt; &amp;&#160;</td>
 
755
          <td class="paramname"><em>features</em>, </td>
 
756
        </tr>
 
757
        <tr>
 
758
          <td class="paramkey"></td>
 
759
          <td></td>
 
760
          <td class="paramtype"><a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a>&lt;&gt; &amp;&#160;</td>
 
761
          <td class="paramname"><em>next_features</em>, </td>
 
762
        </tr>
 
763
        <tr>
 
764
          <td class="paramkey"></td>
 
765
          <td></td>
 
766
          <td class="paramtype"><a class="el" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a>&#160;</td>
 
767
          <td class="paramname"><em>number</em>, </td>
 
768
        </tr>
 
769
        <tr>
 
770
          <td class="paramkey"></td>
 
771
          <td></td>
 
772
          <td class="paramtype"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> &amp;&#160;</td>
 
773
          <td class="paramname"><em>rt</em>&#160;</td>
 
774
        </tr>
 
775
        <tr>
 
776
          <td></td>
 
777
          <td>)</td>
 
778
          <td></td><td></td>
 
779
        </tr>
 
780
      </table>
 
781
</div><div class="memdoc">
 
782
 
 
783
</div>
 
784
</div>
 
785
<a class="anchor" id="add0a01651d44ed438fd2d9202013c2b4"></a>
 
786
<div class="memitem">
 
787
<div class="memproto">
 
788
<table class="mlabels">
 
789
  <tr>
 
790
  <td class="mlabels-left">
 
791
      <table class="memname">
 
792
        <tr>
 
793
          <td class="memname">const std::map&lt;<a class="el" href="classOpenMS_1_1String.html">String</a>, std::set&lt;<a class="el" href="classOpenMS_1_1String.html">String</a>&gt; &gt;&amp; getPeptideProteinCounter </td>
 
794
          <td>(</td>
 
795
          <td class="paramname"></td><td>)</td>
 
796
          <td></td>
 
797
        </tr>
 
798
      </table>
 
799
  </td>
 
800
  <td class="mlabels-right">
 
801
<span class="mlabels"><span class="mlabel">inline</span></span>  </td>
 
802
  </tr>
 
803
</table>
 
804
</div><div class="memdoc">
 
805
 
 
806
</div>
 
807
</div>
 
808
<a class="anchor" id="aea9e9fe1f13d14873c765ddec8f38150"></a>
 
809
<div class="memitem">
 
810
<div class="memproto">
 
811
      <table class="memname">
 
812
        <tr>
 
813
          <td class="memname">void rescore </td>
 
814
          <td>(</td>
 
815
          <td class="paramtype"><a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a>&lt;&gt; &amp;&#160;</td>
 
816
          <td class="paramname"><em>features</em>, </td>
 
817
        </tr>
 
818
        <tr>
 
819
          <td class="paramkey"></td>
 
820
          <td></td>
 
821
          <td class="paramtype">std::vector&lt; <a class="el" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> &gt; &amp;&#160;</td>
 
822
          <td class="paramname"><em>new_pep_ids</em>, </td>
 
823
        </tr>
 
824
        <tr>
 
825
          <td class="paramkey"></td>
 
826
          <td></td>
 
827
          <td class="paramtype">std::vector&lt; <a class="el" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a> &gt; &amp;&#160;</td>
 
828
          <td class="paramname"><em>prot_ids</em>, </td>
 
829
        </tr>
 
830
        <tr>
 
831
          <td class="paramkey"></td>
 
832
          <td></td>
 
833
          <td class="paramtype"><a class="el" href="classOpenMS_1_1PrecursorIonSelectionPreprocessing.html">PrecursorIonSelectionPreprocessing</a> &amp;&#160;</td>
 
834
          <td class="paramname"><em>preprocessed_db</em>, </td>
 
835
        </tr>
 
836
        <tr>
 
837
          <td class="paramkey"></td>
 
838
          <td></td>
 
839
          <td class="paramtype">bool&#160;</td>
 
840
          <td class="paramname"><em>check_meta_values</em> = <code>true</code>&#160;</td>
 
841
        </tr>
 
842
        <tr>
 
843
          <td></td>
 
844
          <td>)</td>
 
845
          <td></td><td></td>
 
846
        </tr>
 
847
      </table>
 
848
</div><div class="memdoc">
 
849
 
 
850
<p>Change scoring of features using peptide identifications only from spectra of the last iteration. </p>
 
851
<dl class="params"><dt>Parameters</dt><dd>
 
852
  <table class="params">
 
853
    <tr><td class="paramname">features</td><td><a class="el" href="classOpenMS_1_1FeatureMap.html" title="A container for features. ">FeatureMap</a> with all possible precursors </td></tr>
 
854
    <tr><td class="paramname">new_pep_ids</td><td>Peptide identifications </td></tr>
 
855
    <tr><td class="paramname">preprocessed_db</td><td>Information from preprocessed database Change scoring of features using peptide identifications from all spectra.</td></tr>
 
856
    <tr><td class="paramname">features</td><td><a class="el" href="classOpenMS_1_1FeatureMap.html" title="A container for features. ">FeatureMap</a> with all possible precursors </td></tr>
 
857
    <tr><td class="paramname">new_pep_ids</td><td>Peptide identifications </td></tr>
 
858
    <tr><td class="paramname">prot_ids</td><td>Protein identifications </td></tr>
 
859
    <tr><td class="paramname">preprocessed_db</td><td>Information from preprocessed database </td></tr>
 
860
    <tr><td class="paramname">check_meta_values</td><td>True if the <a class="el" href="classOpenMS_1_1FeatureMap.html" title="A container for features. ">FeatureMap</a> should be checked for the presence of required meta values </td></tr>
 
861
  </table>
 
862
  </dd>
 
863
</dl>
 
864
 
 
865
</div>
 
866
</div>
 
867
<a class="anchor" id="a75c7dfe3f9c66bb88cddfa8114f4bf3a"></a>
 
868
<div class="memitem">
 
869
<div class="memproto">
 
870
<table class="mlabels">
 
871
  <tr>
 
872
  <td class="mlabels-left">
 
873
      <table class="memname">
 
874
        <tr>
 
875
          <td class="memname">void rescore_ </td>
 
876
          <td>(</td>
 
877
          <td class="paramtype"><a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a>&lt;&gt; &amp;&#160;</td>
 
878
          <td class="paramname"><em>features</em>, </td>
 
879
        </tr>
 
880
        <tr>
 
881
          <td class="paramkey"></td>
 
882
          <td></td>
 
883
          <td class="paramtype">std::vector&lt; <a class="el" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> &gt; &amp;&#160;</td>
 
884
          <td class="paramname"><em>new_pep_ids</em>, </td>
 
885
        </tr>
 
886
        <tr>
 
887
          <td class="paramkey"></td>
 
888
          <td></td>
 
889
          <td class="paramtype"><a class="el" href="classOpenMS_1_1PrecursorIonSelectionPreprocessing.html">PrecursorIonSelectionPreprocessing</a> &amp;&#160;</td>
 
890
          <td class="paramname"><em>preprocessed_db</em>, </td>
 
891
        </tr>
 
892
        <tr>
 
893
          <td class="paramkey"></td>
 
894
          <td></td>
 
895
          <td class="paramtype"><a class="el" href="classOpenMS_1_1PSProteinInference.html">PSProteinInference</a> &amp;&#160;</td>
 
896
          <td class="paramname"><em>protein_inference</em>&#160;</td>
 
897
        </tr>
 
898
        <tr>
 
899
          <td></td>
 
900
          <td>)</td>
 
901
          <td></td><td></td>
 
902
        </tr>
 
903
      </table>
 
904
  </td>
 
905
  <td class="mlabels-right">
 
906
<span class="mlabels"><span class="mlabel">private</span></span>  </td>
 
907
  </tr>
 
908
</table>
 
909
</div><div class="memdoc">
 
910
 
 
911
</div>
 
912
</div>
 
913
<a class="anchor" id="ad20897c5c8bd47f5d4005989bead0e55"></a>
 
914
<div class="memitem">
 
915
<div class="memproto">
 
916
      <table class="memname">
 
917
        <tr>
 
918
          <td class="memname">void reset </td>
 
919
          <td>(</td>
 
920
          <td class="paramname"></td><td>)</td>
 
921
          <td></td>
 
922
        </tr>
 
923
      </table>
 
924
</div><div class="memdoc">
 
925
 
 
926
</div>
 
927
</div>
 
928
<a class="anchor" id="a2b206fdbe8649b90b854129f37fc594a"></a>
 
929
<div class="memitem">
 
930
<div class="memproto">
 
931
<table class="mlabels">
 
932
  <tr>
 
933
  <td class="mlabels-left">
 
934
      <table class="memname">
 
935
        <tr>
 
936
          <td class="memname">void setLPSolver </td>
 
937
          <td>(</td>
 
938
          <td class="paramtype"><a class="el" href="classOpenMS_1_1LPWrapper.html#ab659f8690ca779b8c3d73fe524a39a00">LPWrapper::SOLVER</a>&#160;</td>
 
939
          <td class="paramname"><em>solver</em></td><td>)</td>
 
940
          <td></td>
 
941
        </tr>
 
942
      </table>
 
943
  </td>
 
944
  <td class="mlabels-right">
 
945
<span class="mlabels"><span class="mlabel">inline</span></span>  </td>
 
946
  </tr>
 
947
</table>
 
948
</div><div class="memdoc">
 
949
 
 
950
</div>
 
951
</div>
 
952
<a class="anchor" id="ad3a5be860a268a2fa37776730d91fbc9"></a>
 
953
<div class="memitem">
 
954
<div class="memproto">
 
955
      <table class="memname">
 
956
        <tr>
 
957
          <td class="memname">void setMaxScore </td>
 
958
          <td>(</td>
 
959
          <td class="paramtype">const <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> &amp;&#160;</td>
 
960
          <td class="paramname"><em>max_score</em></td><td>)</td>
 
961
          <td></td>
 
962
        </tr>
 
963
      </table>
 
964
</div><div class="memdoc">
 
965
 
 
966
</div>
 
967
</div>
 
968
<a class="anchor" id="af24d8073d250328ea7b8b7fcd66258c1"></a>
 
969
<div class="memitem">
 
970
<div class="memproto">
 
971
<table class="mlabels">
 
972
  <tr>
 
973
  <td class="mlabels-left">
 
974
      <table class="memname">
 
975
        <tr>
 
976
          <td class="memname">void shiftDown_ </td>
 
977
          <td>(</td>
 
978
          <td class="paramtype"><a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a>&lt;&gt; &amp;&#160;</td>
 
979
          <td class="paramname"><em>features</em>, </td>
 
980
        </tr>
 
981
        <tr>
 
982
          <td class="paramkey"></td>
 
983
          <td></td>
 
984
          <td class="paramtype"><a class="el" href="classOpenMS_1_1PrecursorIonSelectionPreprocessing.html">PrecursorIonSelectionPreprocessing</a> &amp;&#160;</td>
 
985
          <td class="paramname"><em>preprocessed_db</em>, </td>
 
986
        </tr>
 
987
        <tr>
 
988
          <td class="paramkey"></td>
 
989
          <td></td>
 
990
          <td class="paramtype"><a class="el" href="classOpenMS_1_1String.html">String</a>&#160;</td>
 
991
          <td class="paramname"><em>protein_acc</em>&#160;</td>
 
992
        </tr>
 
993
        <tr>
 
994
          <td></td>
 
995
          <td>)</td>
 
996
          <td></td><td></td>
 
997
        </tr>
 
998
      </table>
 
999
  </td>
 
1000
  <td class="mlabels-right">
 
1001
<span class="mlabels"><span class="mlabel">private</span></span>  </td>
 
1002
  </tr>
 
1003
</table>
 
1004
</div><div class="memdoc">
 
1005
 
 
1006
</div>
 
1007
</div>
 
1008
<a class="anchor" id="a624fa4337b310adc1d7b5a2cd046284b"></a>
 
1009
<div class="memitem">
 
1010
<div class="memproto">
 
1011
<table class="mlabels">
 
1012
  <tr>
 
1013
  <td class="mlabels-left">
 
1014
      <table class="memname">
 
1015
        <tr>
 
1016
          <td class="memname">void shiftUp_ </td>
 
1017
          <td>(</td>
 
1018
          <td class="paramtype"><a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a>&lt;&gt; &amp;&#160;</td>
 
1019
          <td class="paramname"><em>features</em>, </td>
 
1020
        </tr>
 
1021
        <tr>
 
1022
          <td class="paramkey"></td>
 
1023
          <td></td>
 
1024
          <td class="paramtype"><a class="el" href="classOpenMS_1_1PrecursorIonSelectionPreprocessing.html">PrecursorIonSelectionPreprocessing</a> &amp;&#160;</td>
 
1025
          <td class="paramname"><em>preprocessed_db</em>, </td>
 
1026
        </tr>
 
1027
        <tr>
 
1028
          <td class="paramkey"></td>
 
1029
          <td></td>
 
1030
          <td class="paramtype"><a class="el" href="classOpenMS_1_1String.html">String</a>&#160;</td>
 
1031
          <td class="paramname"><em>protein_acc</em>&#160;</td>
 
1032
        </tr>
 
1033
        <tr>
 
1034
          <td></td>
 
1035
          <td>)</td>
 
1036
          <td></td><td></td>
 
1037
        </tr>
 
1038
      </table>
 
1039
  </td>
 
1040
  <td class="mlabels-right">
 
1041
<span class="mlabels"><span class="mlabel">private</span></span>  </td>
 
1042
  </tr>
 
1043
</table>
 
1044
</div><div class="memdoc">
 
1045
 
 
1046
</div>
 
1047
</div>
 
1048
<a class="anchor" id="a6d925990e26343cecf35b765b3ee8eda"></a>
 
1049
<div class="memitem">
 
1050
<div class="memproto">
 
1051
<table class="mlabels">
 
1052
  <tr>
 
1053
  <td class="mlabels-left">
 
1054
      <table class="memname">
 
1055
        <tr>
 
1056
          <td class="memname">void simulateILPBasedIPSRun_ </td>
 
1057
          <td>(</td>
 
1058
          <td class="paramtype"><a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a>&lt;&gt; &amp;&#160;</td>
 
1059
          <td class="paramname"><em>features</em>, </td>
 
1060
        </tr>
 
1061
        <tr>
 
1062
          <td class="paramkey"></td>
 
1063
          <td></td>
 
1064
          <td class="paramtype"><a class="el" href="classOpenMS_1_1MSExperiment.html">MSExperiment</a>&lt;&gt; &amp;&#160;</td>
 
1065
          <td class="paramname"><em>experiment</em>, </td>
 
1066
        </tr>
 
1067
        <tr>
 
1068
          <td class="paramkey"></td>
 
1069
          <td></td>
 
1070
          <td class="paramtype">std::vector&lt; <a class="el" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> &gt; &amp;&#160;</td>
 
1071
          <td class="paramname"><em>pep_ids</em>, </td>
 
1072
        </tr>
 
1073
        <tr>
 
1074
          <td class="paramkey"></td>
 
1075
          <td></td>
 
1076
          <td class="paramtype">std::vector&lt; <a class="el" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a> &gt; &amp;&#160;</td>
 
1077
          <td class="paramname"><em>prot_ids</em>, </td>
 
1078
        </tr>
 
1079
        <tr>
 
1080
          <td class="paramkey"></td>
 
1081
          <td></td>
 
1082
          <td class="paramtype"><a class="el" href="classOpenMS_1_1PrecursorIonSelectionPreprocessing.html">PrecursorIonSelectionPreprocessing</a> &amp;&#160;</td>
 
1083
          <td class="paramname"><em>preprocessed_db</em>, </td>
 
1084
        </tr>
 
1085
        <tr>
 
1086
          <td class="paramkey"></td>
 
1087
          <td></td>
 
1088
          <td class="paramtype"><a class="el" href="classOpenMS_1_1String.html">String</a>&#160;</td>
 
1089
          <td class="paramname"><em>output_path</em>, </td>
 
1090
        </tr>
 
1091
        <tr>
 
1092
          <td class="paramkey"></td>
 
1093
          <td></td>
 
1094
          <td class="paramtype"><a class="el" href="classOpenMS_1_1String.html">String</a>&#160;</td>
 
1095
          <td class="paramname"><em>precursor_path</em> = <code>&quot;&quot;</code>&#160;</td>
 
1096
        </tr>
 
1097
        <tr>
 
1098
          <td></td>
 
1099
          <td>)</td>
 
1100
          <td></td><td></td>
 
1101
        </tr>
 
1102
      </table>
 
1103
  </td>
 
1104
  <td class="mlabels-right">
 
1105
<span class="mlabels"><span class="mlabel">private</span></span>  </td>
 
1106
  </tr>
 
1107
</table>
 
1108
</div><div class="memdoc">
 
1109
 
 
1110
</div>
 
1111
</div>
 
1112
<a class="anchor" id="a990b40a17cf86c4b1f3f8d081a9c77c5"></a>
 
1113
<div class="memitem">
 
1114
<div class="memproto">
 
1115
      <table class="memname">
 
1116
        <tr>
 
1117
          <td class="memname">void simulateRun </td>
 
1118
          <td>(</td>
 
1119
          <td class="paramtype"><a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a>&lt;&gt; &amp;&#160;</td>
 
1120
          <td class="paramname"><em>features</em>, </td>
 
1121
        </tr>
 
1122
        <tr>
 
1123
          <td class="paramkey"></td>
 
1124
          <td></td>
 
1125
          <td class="paramtype">std::vector&lt; <a class="el" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> &gt; &amp;&#160;</td>
 
1126
          <td class="paramname"><em>pep_ids</em>, </td>
 
1127
        </tr>
 
1128
        <tr>
 
1129
          <td class="paramkey"></td>
 
1130
          <td></td>
 
1131
          <td class="paramtype">std::vector&lt; <a class="el" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a> &gt; &amp;&#160;</td>
 
1132
          <td class="paramname"><em>prot_ids</em>, </td>
 
1133
        </tr>
 
1134
        <tr>
 
1135
          <td class="paramkey"></td>
 
1136
          <td></td>
 
1137
          <td class="paramtype"><a class="el" href="classOpenMS_1_1PrecursorIonSelectionPreprocessing.html">PrecursorIonSelectionPreprocessing</a> &amp;&#160;</td>
 
1138
          <td class="paramname"><em>preprocessed_db</em>, </td>
 
1139
        </tr>
 
1140
        <tr>
 
1141
          <td class="paramkey"></td>
 
1142
          <td></td>
 
1143
          <td class="paramtype"><a class="el" href="classOpenMS_1_1String.html">String</a>&#160;</td>
 
1144
          <td class="paramname"><em>path</em>, </td>
 
1145
        </tr>
 
1146
        <tr>
 
1147
          <td class="paramkey"></td>
 
1148
          <td></td>
 
1149
          <td class="paramtype"><a class="el" href="classOpenMS_1_1MSExperiment.html">MSExperiment</a>&lt;&gt; &amp;&#160;</td>
 
1150
          <td class="paramname"><em>experiment</em>, </td>
 
1151
        </tr>
 
1152
        <tr>
 
1153
          <td class="paramkey"></td>
 
1154
          <td></td>
 
1155
          <td class="paramtype"><a class="el" href="classOpenMS_1_1String.html">String</a>&#160;</td>
 
1156
          <td class="paramname"><em>precursor_path</em> = <code>&quot;&quot;</code>&#160;</td>
 
1157
        </tr>
 
1158
        <tr>
 
1159
          <td></td>
 
1160
          <td>)</td>
 
1161
          <td></td><td></td>
 
1162
        </tr>
 
1163
      </table>
 
1164
</div><div class="memdoc">
 
1165
 
 
1166
<p>Simulate the iterative precursor ion selection. </p>
 
1167
<dl class="params"><dt>Parameters</dt><dd>
 
1168
  <table class="params">
 
1169
    <tr><td class="paramname">features</td><td><a class="el" href="classOpenMS_1_1FeatureMap.html" title="A container for features. ">FeatureMap</a> with all possible precursors </td></tr>
 
1170
    <tr><td class="paramname">pep_ids</td><td>Peptide identifications </td></tr>
 
1171
    <tr><td class="paramname">prot_ids</td><td>Protein identifications </td></tr>
 
1172
    <tr><td class="paramname">preprocessed_db</td><td>Information from preprocessed database </td></tr>
 
1173
    <tr><td class="paramname">step_size</td><td>Number of MS/MS spectra considered per iteration </td></tr>
 
1174
    <tr><td class="paramname">path</td><td>Path to output file </td></tr>
 
1175
  </table>
 
1176
  </dd>
 
1177
</dl>
 
1178
 
 
1179
</div>
 
1180
</div>
 
1181
<a class="anchor" id="acb2e29dc60d50478abfdf1c85de60b37"></a>
 
1182
<div class="memitem">
 
1183
<div class="memproto">
 
1184
<table class="mlabels">
 
1185
  <tr>
 
1186
  <td class="mlabels-left">
 
1187
      <table class="memname">
 
1188
        <tr>
 
1189
          <td class="memname">void simulateRun_ </td>
 
1190
          <td>(</td>
 
1191
          <td class="paramtype"><a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a>&lt;&gt; &amp;&#160;</td>
 
1192
          <td class="paramname"><em>features</em>, </td>
 
1193
        </tr>
 
1194
        <tr>
 
1195
          <td class="paramkey"></td>
 
1196
          <td></td>
 
1197
          <td class="paramtype">std::vector&lt; <a class="el" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> &gt; &amp;&#160;</td>
 
1198
          <td class="paramname"><em>pep_ids</em>, </td>
 
1199
        </tr>
 
1200
        <tr>
 
1201
          <td class="paramkey"></td>
 
1202
          <td></td>
 
1203
          <td class="paramtype">std::vector&lt; <a class="el" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a> &gt; &amp;&#160;</td>
 
1204
          <td class="paramname"><em>prot_ids</em>, </td>
 
1205
        </tr>
 
1206
        <tr>
 
1207
          <td class="paramkey"></td>
 
1208
          <td></td>
 
1209
          <td class="paramtype"><a class="el" href="classOpenMS_1_1PrecursorIonSelectionPreprocessing.html">PrecursorIonSelectionPreprocessing</a> &amp;&#160;</td>
 
1210
          <td class="paramname"><em>preprocessed_db</em>, </td>
 
1211
        </tr>
 
1212
        <tr>
 
1213
          <td class="paramkey"></td>
 
1214
          <td></td>
 
1215
          <td class="paramtype"><a class="el" href="classOpenMS_1_1String.html">String</a>&#160;</td>
 
1216
          <td class="paramname"><em>path</em>, </td>
 
1217
        </tr>
 
1218
        <tr>
 
1219
          <td class="paramkey"></td>
 
1220
          <td></td>
 
1221
          <td class="paramtype"><a class="el" href="classOpenMS_1_1String.html">String</a>&#160;</td>
 
1222
          <td class="paramname"><em>precursor_path</em> = <code>&quot;&quot;</code>&#160;</td>
 
1223
        </tr>
 
1224
        <tr>
 
1225
          <td></td>
 
1226
          <td>)</td>
 
1227
          <td></td><td></td>
 
1228
        </tr>
 
1229
      </table>
 
1230
  </td>
 
1231
  <td class="mlabels-right">
 
1232
<span class="mlabels"><span class="mlabel">private</span></span>  </td>
 
1233
  </tr>
 
1234
</table>
 
1235
</div><div class="memdoc">
 
1236
 
 
1237
</div>
 
1238
</div>
 
1239
<a class="anchor" id="a2c348a002bfdedc62091f660a1dc2ad3"></a>
 
1240
<div class="memitem">
 
1241
<div class="memproto">
 
1242
<table class="mlabels">
 
1243
  <tr>
 
1244
  <td class="mlabels-left">
 
1245
      <table class="memname">
 
1246
        <tr>
 
1247
          <td class="memname">void sortByTotalScore </td>
 
1248
          <td>(</td>
 
1249
          <td class="paramtype"><a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a>&lt;&gt; &amp;&#160;</td>
 
1250
          <td class="paramname"><em>features</em></td><td>)</td>
 
1251
          <td></td>
 
1252
        </tr>
 
1253
      </table>
 
1254
  </td>
 
1255
  <td class="mlabels-right">
 
1256
<span class="mlabels"><span class="mlabel">inline</span></span>  </td>
 
1257
  </tr>
 
1258
</table>
 
1259
</div><div class="memdoc">
 
1260
 
 
1261
<p>Sort features by total score. </p>
 
1262
 
 
1263
</div>
 
1264
</div>
 
1265
<a class="anchor" id="aaf258e1a9846d9b238ee4b3005ad3ee9"></a>
 
1266
<div class="memitem">
 
1267
<div class="memproto">
 
1268
<table class="mlabels">
 
1269
  <tr>
 
1270
  <td class="mlabels-left">
 
1271
      <table class="memname">
 
1272
        <tr>
 
1273
          <td class="memname">void updateMembers_ </td>
 
1274
          <td>(</td>
 
1275
          <td class="paramname"></td><td>)</td>
 
1276
          <td></td>
 
1277
        </tr>
 
1278
      </table>
 
1279
  </td>
 
1280
  <td class="mlabels-right">
 
1281
<span class="mlabels"><span class="mlabel">private</span><span class="mlabel">virtual</span></span>  </td>
 
1282
  </tr>
 
1283
</table>
 
1284
</div><div class="memdoc">
 
1285
 
 
1286
<p>update members method from <a class="el" href="classOpenMS_1_1DefaultParamHandler.html" title="A base class for all classes handling default parameters. ">DefaultParamHandler</a> to update the members </p>
 
1287
 
 
1288
<p>Reimplemented from <a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a776f7572fc4f466e9527ca233471920d">DefaultParamHandler</a>.</p>
 
1289
 
 
1290
</div>
 
1291
</div>
 
1292
<h2 class="groupheader">Member Data Documentation</h2>
 
1293
<a class="anchor" id="a0d138c04b4994b24723c3d3fc7d76209"></a>
 
1294
<div class="memitem">
 
1295
<div class="memproto">
 
1296
<table class="mlabels">
 
1297
  <tr>
 
1298
  <td class="mlabels-left">
 
1299
      <table class="memname">
 
1300
        <tr>
 
1301
          <td class="memname">std::vector&lt;<a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a>&gt; fraction_counter_</td>
 
1302
        </tr>
 
1303
      </table>
 
1304
  </td>
 
1305
  <td class="mlabels-right">
 
1306
<span class="mlabels"><span class="mlabel">private</span></span>  </td>
 
1307
  </tr>
 
1308
</table>
 
1309
</div><div class="memdoc">
 
1310
 
 
1311
<p>stores the number of selected precursors per fraction </p>
 
1312
 
 
1313
</div>
 
1314
</div>
 
1315
<a class="anchor" id="a78c0d505b8706df48e8cf696e21035ee"></a>
 
1316
<div class="memitem">
 
1317
<div class="memproto">
 
1318
<table class="mlabels">
 
1319
  <tr>
 
1320
  <td class="mlabels-left">
 
1321
      <table class="memname">
 
1322
        <tr>
 
1323
          <td class="memname"><a class="el" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a> max_iteration_</td>
 
1324
        </tr>
 
1325
      </table>
 
1326
  </td>
 
1327
  <td class="mlabels-right">
 
1328
<span class="mlabels"><span class="mlabel">private</span></span>  </td>
 
1329
  </tr>
 
1330
</table>
 
1331
</div><div class="memdoc">
 
1332
 
 
1333
<p>maximal number of iterations </p>
 
1334
 
 
1335
</div>
 
1336
</div>
 
1337
<a class="anchor" id="a350439a140c1f53c49e6a414063bec95"></a>
 
1338
<div class="memitem">
 
1339
<div class="memproto">
 
1340
<table class="mlabels">
 
1341
  <tr>
 
1342
  <td class="mlabels-left">
 
1343
      <table class="memname">
 
1344
        <tr>
 
1345
          <td class="memname"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> max_score_</td>
 
1346
        </tr>
 
1347
      </table>
 
1348
  </td>
 
1349
  <td class="mlabels-right">
 
1350
<span class="mlabels"><span class="mlabel">private</span></span>  </td>
 
1351
  </tr>
 
1352
</table>
 
1353
</div><div class="memdoc">
 
1354
 
 
1355
<p>maximal score in the <a class="el" href="classOpenMS_1_1FeatureMap.html" title="A container for features. ">FeatureMap</a> </p>
 
1356
 
 
1357
</div>
 
1358
</div>
 
1359
<a class="anchor" id="a1d33655f6c9055337571b352a0f8c688"></a>
 
1360
<div class="memitem">
 
1361
<div class="memproto">
 
1362
<table class="mlabels">
 
1363
  <tr>
 
1364
  <td class="mlabels-left">
 
1365
      <table class="memname">
 
1366
        <tr>
 
1367
          <td class="memname"><a class="el" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a> min_pep_ids_</td>
 
1368
        </tr>
 
1369
      </table>
 
1370
  </td>
 
1371
  <td class="mlabels-right">
 
1372
<span class="mlabels"><span class="mlabel">private</span></span>  </td>
 
1373
  </tr>
 
1374
</table>
 
1375
</div><div class="memdoc">
 
1376
 
 
1377
<p>minimal number of peptides identified for a protein to be declared identified </p>
 
1378
 
 
1379
</div>
 
1380
</div>
 
1381
<a class="anchor" id="aa0d44a6be23374eb5d1f099ef8b4ca82"></a>
 
1382
<div class="memitem">
 
1383
<div class="memproto">
 
1384
<table class="mlabels">
 
1385
  <tr>
 
1386
  <td class="mlabels-left">
 
1387
      <table class="memname">
 
1388
        <tr>
 
1389
          <td class="memname"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> mz_tolerance_</td>
 
1390
        </tr>
 
1391
      </table>
 
1392
  </td>
 
1393
  <td class="mlabels-right">
 
1394
<span class="mlabels"><span class="mlabel">private</span></span>  </td>
 
1395
  </tr>
 
1396
</table>
 
1397
</div><div class="memdoc">
 
1398
 
 
1399
<p>precursor ion error tolerance </p>
 
1400
 
 
1401
</div>
 
1402
</div>
 
1403
<a class="anchor" id="a05ce08b9b0435cc41cb9f2528c313237"></a>
 
1404
<div class="memitem">
 
1405
<div class="memproto">
 
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          <td class="memname"><a class="el" href="classOpenMS_1_1String.html">String</a> mz_tolerance_unit_</td>
 
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        </tr>
 
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<p>precursor ion error tolerance unit (ppm or Da) </p>
 
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</div>
 
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</div>
 
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<a class="anchor" id="ae7c765448d55eedc24f212e92602a8ec"></a>
 
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          <td class="memname">std::map&lt;<a class="el" href="classOpenMS_1_1String.html">String</a>, std::set&lt;<a class="el" href="classOpenMS_1_1String.html">String</a>&gt; &gt; prot_id_counter_</td>
 
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<p>stores the peptide sequences for all protein identifications </p>
 
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</div>
 
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</div>
 
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<a class="anchor" id="afb8f1202d548f01394d85fbeb51f9adf"></a>
 
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          <td class="memname"><a class="el" href="classOpenMS_1_1LPWrapper.html#ab659f8690ca779b8c3d73fe524a39a00">LPWrapper::SOLVER</a> solver_</td>
 
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<a class="anchor" id="ae96b07c06ceff094f476fd92cbe89e10"></a>
 
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          <td class="memname"><a class="el" href="classOpenMS_1_1PrecursorIonSelection.html#a1d1cfd8ffb84e947f82999c682b666a7">Type</a> type_</td>
 
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        </tr>
 
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<p>precursor ion selection strategy </p>
 
1486
 
 
1487
</div>
 
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<a class="anchor" id="a3ff6e92379e0c12cecff4f086c60b0b7"></a>
 
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          <td class="memname"><a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> x_variable_number_</td>
 
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</div><!-- contents -->
 
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<HR style="height:1px; border:none; border-top:1px solid #c0c0c0;">
 
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<TABLE width="100%" border="0">
 
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<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
 
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<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:27 using doxygen 1.8.5</font></TD>
 
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