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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_1InclusionExclusionList.html
 
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<HTML>
 
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<HEAD>
 
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<TITLE>InclusionExclusionList Class Reference</TITLE>
 
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<LINK HREF="doxygen.css" REL="stylesheet" TYPE="text/css">
 
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<LINK HREF="style_ini.css" REL="stylesheet" TYPE="text/css">
 
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</HEAD>
 
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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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<!-- Generated by Doxygen 1.8.5 -->
 
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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_1InclusionExclusionList.html">InclusionExclusionList</a></li>  </ul>
 
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</div>
 
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</div><!-- top -->
 
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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-methods">Public Member Functions</a> &#124;
 
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<a href="#pro-types">Protected Types</a> &#124;
 
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<a href="#pro-methods">Protected Member Functions</a> &#124;
 
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<a href="classOpenMS_1_1InclusionExclusionList-members.html">List of all members</a>  </div>
 
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  <div class="headertitle">
 
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<div class="title">InclusionExclusionList Class Reference</div>  </div>
 
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</div><!--header-->
 
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<div class="contents">
 
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<p>Provides functionalty for writing inclusion or exclusion lists.  
 
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 <a href="classOpenMS_1_1InclusionExclusionList.html#details">More...</a></p>
 
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<p><code>#include &lt;<a class="el" href="InclusionExclusionList_8h_source.html">OpenMS/ANALYSIS/TARGETED/InclusionExclusionList.h</a>&gt;</code></p>
 
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<div class="dynheader">
 
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Inheritance diagram for InclusionExclusionList:</div>
 
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<div class="dyncontent">
 
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 <div class="center">
 
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  <img src="classOpenMS_1_1InclusionExclusionList.png" usemap="#InclusionExclusionList_map" alt=""/>
 
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  <map id="InclusionExclusionList_map" name="InclusionExclusionList_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="0,0,135,24"/>
 
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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_1InclusionExclusionList_1_1IEWindow.html">IEWindow</a></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">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1InclusionExclusionList_1_1WindowDistance__.html">WindowDistance_</a></td></tr>
 
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<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight">Determine distance between two spectra.  <a href="classOpenMS_1_1InclusionExclusionList_1_1WindowDistance__.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-methods"></a>
 
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Public Member Functions</h2></td></tr>
 
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<tr class="memitem:a3a8d40df2e4287faecbad66300ffafb5"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1InclusionExclusionList.html#a3a8d40df2e4287faecbad66300ffafb5">writeTargets</a> (const std::vector&lt; <a class="el" href="structOpenMS_1_1FASTAFile_1_1FASTAEntry.html">FASTAFile::FASTAEntry</a> &gt; &amp;fasta_entries, const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;out_path, const <a class="el" href="classOpenMS_1_1IntList.html">IntList</a> &amp;charges, const <a class="el" href="classOpenMS_1_1String.html">String</a> rt_model_path)</td></tr>
 
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<tr class="memdesc:a3a8d40df2e4287faecbad66300ffafb5"><td class="mdescLeft">&#160;</td><td class="mdescRight">Writes inclusion or exclusion list of tryptic peptides of the given proteins (tab-delimited).  <a href="#a3a8d40df2e4287faecbad66300ffafb5">More...</a><br/></td></tr>
 
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<tr class="separator:a3a8d40df2e4287faecbad66300ffafb5"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<tr class="memitem:a2ce3209b3f0366b9f02b5ab21ec2b86c"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1InclusionExclusionList.html#a2ce3209b3f0366b9f02b5ab21ec2b86c">writeTargets</a> (const <a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a>&lt;&gt; &amp;map, const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;out_path)</td></tr>
 
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<tr class="memdesc:a2ce3209b3f0366b9f02b5ab21ec2b86c"><td class="mdescLeft">&#160;</td><td class="mdescRight">Writes inclusion or exclusion list of given feature map.  <a href="#a2ce3209b3f0366b9f02b5ab21ec2b86c">More...</a><br/></td></tr>
 
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<tr class="separator:a2ce3209b3f0366b9f02b5ab21ec2b86c"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<tr class="memitem:a31048972ba4d36a0e25beef7f018f9ca"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1InclusionExclusionList.html#a31048972ba4d36a0e25beef7f018f9ca">writeTargets</a> (const std::vector&lt; <a class="el" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> &gt; &amp;pep_ids, const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;out_path, const <a class="el" href="classOpenMS_1_1IntList.html">IntList</a> &amp;charges)</td></tr>
 
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<tr class="memdesc:a31048972ba4d36a0e25beef7f018f9ca"><td class="mdescLeft">&#160;</td><td class="mdescRight">Writes inclusion or exclusion list of given peptide ids (tab-delimited).  <a href="#a31048972ba4d36a0e25beef7f018f9ca">More...</a><br/></td></tr>
 
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<tr class="separator:a31048972ba4d36a0e25beef7f018f9ca"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<tr><td colspan="2"><div class="groupHeader">Constructors and destructors</div></td></tr>
 
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<tr class="memitem:ae77455151d08007959c4e91000c66a33"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1InclusionExclusionList.html#ae77455151d08007959c4e91000c66a33">InclusionExclusionList</a> ()</td></tr>
 
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<tr class="memdesc:ae77455151d08007959c4e91000c66a33"><td class="mdescLeft">&#160;</td><td class="mdescRight">default constructor  <a href="#ae77455151d08007959c4e91000c66a33">More...</a><br/></td></tr>
 
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<tr class="separator:ae77455151d08007959c4e91000c66a33"><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>
 
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<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>
 
96
<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>
 
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<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>
 
99
<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>
 
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<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="pro-types"></a>
 
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Protected Types</h2></td></tr>
 
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<tr class="memitem:a37ce296761514de1523091ecdc8e138e"><td class="memItemLeft" align="right" valign="top">typedef std::vector&lt; <a class="el" href="structOpenMS_1_1InclusionExclusionList_1_1IEWindow.html">IEWindow</a> &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1InclusionExclusionList.html#a37ce296761514de1523091ecdc8e138e">WindowList</a></td></tr>
 
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<tr class="separator:a37ce296761514de1523091ecdc8e138e"><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="pro-methods"></a>
 
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Protected Member Functions</h2></td></tr>
 
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<tr class="memitem:a60696c69cd1740973caf47341908a94f"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1InclusionExclusionList.html#a60696c69cd1740973caf47341908a94f">mergeOverlappingWindows_</a> (<a class="el" href="classOpenMS_1_1InclusionExclusionList.html#a37ce296761514de1523091ecdc8e138e">WindowList</a> &amp;list) const </td></tr>
 
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<tr class="memdesc:a60696c69cd1740973caf47341908a94f"><td class="mdescLeft">&#160;</td><td class="mdescRight">Merges overlapping windows using m/z tolerance.  <a href="#a60696c69cd1740973caf47341908a94f">More...</a><br/></td></tr>
 
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<tr class="separator:a60696c69cd1740973caf47341908a94f"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<tr class="memitem:a3bf793b4aeff77774abc1a152607b85b"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1InclusionExclusionList.html#a3bf793b4aeff77774abc1a152607b85b">writeToFile_</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;out_path, const <a class="el" href="classOpenMS_1_1InclusionExclusionList.html#a37ce296761514de1523091ecdc8e138e">WindowList</a> &amp;windows) const </td></tr>
 
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<tr class="memdesc:a3bf793b4aeff77774abc1a152607b85b"><td class="mdescLeft">&#160;</td><td class="mdescRight">Writes the windows to the given file.  <a href="#a3bf793b4aeff77774abc1a152607b85b">More...</a><br/></td></tr>
 
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<tr class="separator:a3bf793b4aeff77774abc1a152607b85b"><td class="memSeparator" colspan="2">&#160;</td></tr>
 
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<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:a776f7572fc4f466e9527ca233471920d inherit pro_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">virtual void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a776f7572fc4f466e9527ca233471920d">updateMembers_</a> ()</td></tr>
 
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<tr class="memdesc:a776f7572fc4f466e9527ca233471920d inherit pro_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft">&#160;</td><td class="mdescRight">This method is used to update extra member variables at the end of the <a class="el" href="classOpenMS_1_1DefaultParamHandler.html#abc8067511cfc949ae942ea2b08588f81" title="Sets the parameters. ">setParameters()</a> method.  <a href="#a776f7572fc4f466e9527ca233471920d">More...</a><br/></td></tr>
 
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<tr class="separator:a776f7572fc4f466e9527ca233471920d inherit pro_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2">&#160;</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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</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>
 
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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>
 
130
<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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</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>Provides functionalty for writing inclusion or exclusion lists. </p>
 
151
 <dl class="todo"><dt><b><a class="el" href="todo.html#_todo000003">Todo:</a></b></dt><dd>allow modifications (fixed?) </dd></dl>
 
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</div><h2 class="groupheader">Member Typedef Documentation</h2>
 
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          <td class="memname">typedef std::vector&lt;<a class="el" href="structOpenMS_1_1InclusionExclusionList_1_1IEWindow.html">IEWindow</a>&gt; <a class="el" href="classOpenMS_1_1InclusionExclusionList.html#a37ce296761514de1523091ecdc8e138e">WindowList</a></td>
 
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<span class="mlabels"><span class="mlabel">protected</span></span>  </td>
 
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<h2 class="groupheader">Constructor &amp; Destructor Documentation</h2>
 
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          <td class="memname"><a class="el" href="classOpenMS_1_1InclusionExclusionList.html">InclusionExclusionList</a> </td>
 
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          <td>(</td>
 
181
          <td class="paramname"></td><td>)</td>
 
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          <td></td>
 
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</div><div class="memdoc">
 
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<p>default constructor </p>
 
188
 
 
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</div>
 
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<h2 class="groupheader">Member Function Documentation</h2>
 
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<a class="anchor" id="a60696c69cd1740973caf47341908a94f"></a>
 
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          <td class="memname">void mergeOverlappingWindows_ </td>
 
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          <td>(</td>
 
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          <td class="paramtype"><a class="el" href="classOpenMS_1_1InclusionExclusionList.html#a37ce296761514de1523091ecdc8e138e">WindowList</a> &amp;&#160;</td>
 
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          <td class="paramname"><em>list</em></td><td>)</td>
 
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          <td> const</td>
 
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</div><div class="memdoc">
 
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<p>Merges overlapping windows using m/z tolerance. </p>
 
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<p>We employ single linkage clustering to merge windows that:</p>
 
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<ul>
 
217
<li>are close in m/z</li>
 
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<li>overlap in RT All clusters found by this are merged such that:</li>
 
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<li>RT windows are extended</li>
 
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<li>m/z value is averaged over all windows </li>
 
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</ul>
 
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          <td class="memname">void writeTargets </td>
 
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          <td>(</td>
 
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          <td class="paramtype">const std::vector&lt; <a class="el" href="structOpenMS_1_1FASTAFile_1_1FASTAEntry.html">FASTAFile::FASTAEntry</a> &gt; &amp;&#160;</td>
 
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          <td class="paramname"><em>fasta_entries</em>, </td>
 
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          <td class="paramkey"></td>
 
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          <td></td>
 
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          <td class="paramtype">const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;&#160;</td>
 
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          <td class="paramname"><em>out_path</em>, </td>
 
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          <td></td>
 
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          <td class="paramtype">const <a class="el" href="classOpenMS_1_1IntList.html">IntList</a> &amp;&#160;</td>
 
245
          <td class="paramname"><em>charges</em>, </td>
 
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          <td class="paramkey"></td>
 
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          <td></td>
 
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          <td class="paramtype">const <a class="el" href="classOpenMS_1_1String.html">String</a>&#160;</td>
 
251
          <td class="paramname"><em>rt_model_path</em>&#160;</td>
 
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          <td></td>
 
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          <td>)</td>
 
256
          <td></td><td></td>
 
257
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</div><div class="memdoc">
 
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261
<p>Writes inclusion or exclusion list of tryptic peptides of the given proteins (tab-delimited). </p>
 
262
<dl class="exception"><dt>Exceptions</dt><dd>
 
263
  <table class="exception">
 
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    <tr><td class="paramname"><a class="el" href="classOpenMS_1_1Exception_1_1UnableToCreateFile.html" title="Unable to create file exception. ">Exception::UnableToCreateFile</a></td><td>is thrown if the output file cannot be created </td></tr>
 
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  </table>
 
266
  </dd>
 
267
</dl>
 
268
 
 
269
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<a class="anchor" id="a2ce3209b3f0366b9f02b5ab21ec2b86c"></a>
 
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          <td class="memname">void writeTargets </td>
 
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          <td>(</td>
 
278
          <td class="paramtype">const <a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a>&lt;&gt; &amp;&#160;</td>
 
279
          <td class="paramname"><em>map</em>, </td>
 
280
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        <tr>
 
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          <td class="paramkey"></td>
 
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          <td></td>
 
284
          <td class="paramtype">const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;&#160;</td>
 
285
          <td class="paramname"><em>out_path</em>&#160;</td>
 
286
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287
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          <td></td>
 
289
          <td>)</td>
 
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          <td></td><td></td>
 
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        </tr>
 
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      </table>
 
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</div><div class="memdoc">
 
294
 
 
295
<p>Writes inclusion or exclusion list of given feature map. </p>
 
296
<dl class="exception"><dt>Exceptions</dt><dd>
 
297
  <table class="exception">
 
298
    <tr><td class="paramname"><a class="el" href="classOpenMS_1_1Exception_1_1UnableToCreateFile.html" title="Unable to create file exception. ">Exception::UnableToCreateFile</a></td><td>is thrown if the output file cannot be created </td></tr>
 
299
  </table>
 
300
  </dd>
 
301
</dl>
 
302
 
 
303
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304
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          <td class="memname">void writeTargets </td>
 
311
          <td>(</td>
 
312
          <td class="paramtype">const std::vector&lt; <a class="el" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> &gt; &amp;&#160;</td>
 
313
          <td class="paramname"><em>pep_ids</em>, </td>
 
314
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316
          <td class="paramkey"></td>
 
317
          <td></td>
 
318
          <td class="paramtype">const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;&#160;</td>
 
319
          <td class="paramname"><em>out_path</em>, </td>
 
320
        </tr>
 
321
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322
          <td class="paramkey"></td>
 
323
          <td></td>
 
324
          <td class="paramtype">const <a class="el" href="classOpenMS_1_1IntList.html">IntList</a> &amp;&#160;</td>
 
325
          <td class="paramname"><em>charges</em>&#160;</td>
 
326
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327
        <tr>
 
328
          <td></td>
 
329
          <td>)</td>
 
330
          <td></td><td></td>
 
331
        </tr>
 
332
      </table>
 
333
</div><div class="memdoc">
 
334
 
 
335
<p>Writes inclusion or exclusion list of given peptide ids (tab-delimited). </p>
 
336
<dl class="exception"><dt>Exceptions</dt><dd>
 
337
  <table class="exception">
 
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    <tr><td class="paramname"><a class="el" href="classOpenMS_1_1Exception_1_1UnableToCreateFile.html" title="Unable to create file exception. ">Exception::UnableToCreateFile</a></td><td>is thrown if the output file cannot be created </td></tr>
 
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    <tr><td class="paramname"><a class="el" href="classOpenMS_1_1Exception_1_1InvalidSize.html" title="Invalid UInt exception. ">Exception::InvalidSize</a></td><td>is thrown if a peptide id contains more than one hit </td></tr>
 
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    <tr><td class="paramname"><a class="el" href="classOpenMS_1_1Exception_1_1MissingInformation.html" title="Not all required information provided. ">Exception::MissingInformation</a></td><td>is thrown if a peptide id contains no RT information </td></tr>
 
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          <td class="memname">void writeToFile_ </td>
 
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          <td>(</td>
 
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          <td class="paramtype">const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;&#160;</td>
 
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          <td class="paramname"><em>out_path</em>, </td>
 
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          <td class="paramtype">const <a class="el" href="classOpenMS_1_1InclusionExclusionList.html#a37ce296761514de1523091ecdc8e138e">WindowList</a> &amp;&#160;</td>
 
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          <td class="paramname"><em>windows</em>&#160;</td>
 
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          <td>)</td>
 
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          <td></td><td> const</td>
 
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<span class="mlabels"><span class="mlabel">protected</span></span>  </td>
 
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<p>Writes the windows to the given file. </p>
 
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<p>Format for each window is: &lt;mz&gt;\t&lt;rt_start&gt;\t&lt;rt_stop&gt;\n</p>
 
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<dl class="exception"><dt>Exceptions</dt><dd>
 
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    <tr><td class="paramname"><a class="el" href="classOpenMS_1_1Exception_1_1UnableToCreateFile.html" title="Unable to create file exception. ">Exception::UnableToCreateFile</a></td><td>when file cannot be created </td></tr>
 
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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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