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<HTML>
<HEAD>
<TITLE>TOPPRNPxl Class Reference</TITLE>
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<A href="index.html">Home</A> &nbsp;&middot;
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<!-- Generated by Doxygen 1.8.5 -->
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<div class="header">
  <div class="summary">
<a href="#pub-methods">Public Member Functions</a> &#124;
<a href="#pro-methods">Protected Member Functions</a> &#124;
<a href="classTOPPRNPxl-members.html">List of all members</a>  </div>
  <div class="headertitle">
<div class="title">TOPPRNPxl Class Reference</div>  </div>
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<div class="contents">
<div class="dynheader">
Inheritance diagram for TOPPRNPxl:</div>
<div class="dyncontent">
 <div class="center">
  <img src="classTOPPRNPxl.png" usemap="#TOPPRNPxl_map" alt=""/>
  <map id="TOPPRNPxl_map" name="TOPPRNPxl_map">
<area href="classOpenMS_1_1TOPPBase.html" title="Base class for TOPP applications. " alt="TOPPBase" shape="rect" coords="0,0,79,24"/>
</map>
 </div></div>
<table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
Public Member Functions</h2></td></tr>
<tr class="memitem:abf14ac0ef5097d17e6a377ae89b31772"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classTOPPRNPxl.html#abf14ac0ef5097d17e6a377ae89b31772">TOPPRNPxl</a> ()</td></tr>
<tr class="separator:abf14ac0ef5097d17e6a377ae89b31772"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="inherit_header pub_methods_classOpenMS_1_1TOPPBase"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_classOpenMS_1_1TOPPBase')"><img src="closed.png" alt="-"/>&#160;Public Member Functions inherited from <a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td></tr>
<tr class="memitem:a227f68edf8608ce32984ab7b250f3d38 inherit pub_methods_classOpenMS_1_1TOPPBase"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TOPPBase.html#a227f68edf8608ce32984ab7b250f3d38">TOPPBase</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;name, const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;description, bool official=true, bool id_tag_support=false, bool require_args=true, const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;version=&quot;&quot;)</td></tr>
<tr class="memdesc:a227f68edf8608ce32984ab7b250f3d38 inherit pub_methods_classOpenMS_1_1TOPPBase"><td class="mdescLeft">&#160;</td><td class="mdescRight">Constructor.  <a href="#a227f68edf8608ce32984ab7b250f3d38">More...</a><br/></td></tr>
<tr class="separator:a227f68edf8608ce32984ab7b250f3d38 inherit pub_methods_classOpenMS_1_1TOPPBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a445a6591bf0daa05be19ff3f5dea0f43 inherit pub_methods_classOpenMS_1_1TOPPBase"><td class="memItemLeft" align="right" valign="top">virtual&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TOPPBase.html#a445a6591bf0daa05be19ff3f5dea0f43">~TOPPBase</a> ()</td></tr>
<tr class="memdesc:a445a6591bf0daa05be19ff3f5dea0f43 inherit pub_methods_classOpenMS_1_1TOPPBase"><td class="mdescLeft">&#160;</td><td class="mdescRight">Destructor.  <a href="#a445a6591bf0daa05be19ff3f5dea0f43">More...</a><br/></td></tr>
<tr class="separator:a445a6591bf0daa05be19ff3f5dea0f43 inherit pub_methods_classOpenMS_1_1TOPPBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a6f464153a13b38c04f41b4ec9d9714c5 inherit pub_methods_classOpenMS_1_1TOPPBase"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537">ExitCodes</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TOPPBase.html#a6f464153a13b38c04f41b4ec9d9714c5">main</a> (int argc, const char **argv)</td></tr>
<tr class="memdesc:a6f464153a13b38c04f41b4ec9d9714c5 inherit pub_methods_classOpenMS_1_1TOPPBase"><td class="mdescLeft">&#160;</td><td class="mdescRight">Main routine of all TOPP applications.  <a href="#a6f464153a13b38c04f41b4ec9d9714c5">More...</a><br/></td></tr>
<tr class="separator:a6f464153a13b38c04f41b4ec9d9714c5 inherit pub_methods_classOpenMS_1_1TOPPBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pro-methods"></a>
Protected Member Functions</h2></td></tr>
<tr class="memitem:a3d074eaf7c38c2e730f3afd97c865350"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classTOPPRNPxl.html#a3d074eaf7c38c2e730f3afd97c865350">registerOptionsAndFlags_</a> ()</td></tr>
<tr class="memdesc:a3d074eaf7c38c2e730f3afd97c865350"><td class="mdescLeft">&#160;</td><td class="mdescRight">Sets the valid command line options (with argument) and flags (without argument).  <a href="#a3d074eaf7c38c2e730f3afd97c865350">More...</a><br/></td></tr>
<tr class="separator:a3d074eaf7c38c2e730f3afd97c865350"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ae6668492d67ea303296f9db6ac56325c"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537">ExitCodes</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classTOPPRNPxl.html#ae6668492d67ea303296f9db6ac56325c">main_</a> (int, const char **)</td></tr>
<tr class="memdesc:ae6668492d67ea303296f9db6ac56325c"><td class="mdescLeft">&#160;</td><td class="mdescRight">The actual "main" method. <a class="el" href="classTOPPRNPxl.html#ae6668492d67ea303296f9db6ac56325c" title="The actual &quot;main&quot; method. main_() is invoked by main(). ">main_()</a> is invoked by <a class="el" href="classOpenMS_1_1TOPPBase.html#a6f464153a13b38c04f41b4ec9d9714c5" title="Main routine of all TOPP applications. ">main()</a>.  <a href="#ae6668492d67ea303296f9db6ac56325c">More...</a><br/></td></tr>
<tr class="separator:ae6668492d67ea303296f9db6ac56325c"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="inherit_header pro_methods_classOpenMS_1_1TOPPBase"><td colspan="2" onclick="javascript:toggleInherit('pro_methods_classOpenMS_1_1TOPPBase')"><img src="closed.png" alt="-"/>&#160;Protected Member Functions inherited from <a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td></tr>
<tr class="memitem:ab281176746eb5f3e1ff6441353f0c468 inherit pro_methods_classOpenMS_1_1TOPPBase"><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_1TOPPBase.html#ab281176746eb5f3e1ff6441353f0c468">getIniLocation_</a> () const </td></tr>
<tr class="memdesc:ab281176746eb5f3e1ff6441353f0c468 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="mdescLeft">&#160;</td><td class="mdescRight">Returns the location of the ini file where parameters are taken from. E.g. if the command line was <code>TOPPTool -instance 17</code>, then this will be <code>"TOPPTool:17:"</code>. Note the ':' at the end.  <a href="#ab281176746eb5f3e1ff6441353f0c468">More...</a><br/></td></tr>
<tr class="separator:ab281176746eb5f3e1ff6441353f0c468 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a99657ef10c0478aff846bd9a2ce91ede inherit pro_methods_classOpenMS_1_1TOPPBase"><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_1TOPPBase.html#a99657ef10c0478aff846bd9a2ce91ede">toolName_</a> () const </td></tr>
<tr class="memdesc:a99657ef10c0478aff846bd9a2ce91ede inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="mdescLeft">&#160;</td><td class="mdescRight">Returns the tool name.  <a href="#a99657ef10c0478aff846bd9a2ce91ede">More...</a><br/></td></tr>
<tr class="separator:a99657ef10c0478aff846bd9a2ce91ede inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a48067d9b286e137c0e1a5e7a5ce3ebfc inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TOPPBase.html#a48067d9b286e137c0e1a5e7a5ce3ebfc">printUsage_</a> ()</td></tr>
<tr class="memdesc:a48067d9b286e137c0e1a5e7a5ce3ebfc inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="mdescLeft">&#160;</td><td class="mdescRight">Prints the tool-specific command line options and appends the common options.  <a href="#a48067d9b286e137c0e1a5e7a5ce3ebfc">More...</a><br/></td></tr>
<tr class="separator:a48067d9b286e137c0e1a5e7a5ce3ebfc inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a598f835681c78f5092d4e6603b783cd8 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TOPPBase.html#a598f835681c78f5092d4e6603b783cd8">parseRange_</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;text, <a class="el" href="classdouble.html">double</a> &amp;low, <a class="el" href="classdouble.html">double</a> &amp;high) const </td></tr>
<tr class="memdesc:a598f835681c78f5092d4e6603b783cd8 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="mdescLeft">&#160;</td><td class="mdescRight">Helper function that parses a range string ([a]:[b]) into two variables.  <a href="#a598f835681c78f5092d4e6603b783cd8">More...</a><br/></td></tr>
<tr class="separator:a598f835681c78f5092d4e6603b783cd8 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ac7f9f64984349818c53c9c7b112ba989 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TOPPBase.html#ac7f9f64984349818c53c9c7b112ba989">parseRange_</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;text, <a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> &amp;low, <a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> &amp;high) const </td></tr>
<tr class="memdesc:ac7f9f64984349818c53c9c7b112ba989 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="mdescLeft">&#160;</td><td class="mdescRight">Helper function that parses a range string ([a]:[b]) into two variables.  <a href="#ac7f9f64984349818c53c9c7b112ba989">More...</a><br/></td></tr>
<tr class="separator:ac7f9f64984349818c53c9c7b112ba989 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a51bd3e8ab55a00704b0096e417772a02 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classOpenMS_1_1DocumentIDTagger.html">DocumentIDTagger</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TOPPBase.html#a51bd3e8ab55a00704b0096e417772a02">getDocumentIDTagger_</a> () const </td></tr>
<tr class="memdesc:a51bd3e8ab55a00704b0096e417772a02 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="mdescLeft">&#160;</td><td class="mdescRight">get <a class="el" href="classOpenMS_1_1DocumentIDTagger.html" title="Tags OpenMS file containers with a DocumentID. ">DocumentIDTagger</a> to assign DocumentIDs to maps  <a href="#a51bd3e8ab55a00704b0096e417772a02">More...</a><br/></td></tr>
<tr class="separator:a51bd3e8ab55a00704b0096e417772a02 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ab1a681a54b8c67e9b99bd00e64c3c734 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TOPPBase.html#ab1a681a54b8c67e9b99bd00e64c3c734">writeCTD_</a> ()</td></tr>
<tr class="memdesc:ab1a681a54b8c67e9b99bd00e64c3c734 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="mdescLeft">&#160;</td><td class="mdescRight">Write common tool description (CTD) file.  <a href="#ab1a681a54b8c67e9b99bd00e64c3c734">More...</a><br/></td></tr>
<tr class="separator:ab1a681a54b8c67e9b99bd00e64c3c734 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a36f05bcff0f3b2173f7d5762f071cfe9 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537">ExitCodes</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TOPPBase.html#a36f05bcff0f3b2173f7d5762f071cfe9">writeWSDL_</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;filename)</td></tr>
<tr class="memdesc:a36f05bcff0f3b2173f7d5762f071cfe9 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="mdescLeft">&#160;</td><td class="mdescRight">Write WSDL file and validate it. Returns EXECUTION_OK or INTERNAL_ERROR (if validation failed)  <a href="#a36f05bcff0f3b2173f7d5762f071cfe9">More...</a><br/></td></tr>
<tr class="separator:a36f05bcff0f3b2173f7d5762f071cfe9 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a094f775e91502e30b2acd25d6434f019 inherit pro_methods_classOpenMS_1_1TOPPBase"><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_1TOPPBase.html#a094f775e91502e30b2acd25d6434f019">getParamArgument_</a> (const <a class="el" href="structOpenMS_1_1Param_1_1ParamEntry.html">Param::ParamEntry</a> &amp;entry) const </td></tr>
<tr class="memdesc:a094f775e91502e30b2acd25d6434f019 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="mdescLeft">&#160;</td><td class="mdescRight">Utility function that determines a suitable argument value for the given <a class="el" href="structOpenMS_1_1Param_1_1ParamEntry.html" title="Parameter entry used to store the actual information inside of a Param entry. ">Param::ParamEntry</a>.  <a href="#a094f775e91502e30b2acd25d6434f019">More...</a><br/></td></tr>
<tr class="separator:a094f775e91502e30b2acd25d6434f019 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a60bdece826d183bdadb31c85126c3431 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memItemLeft" align="right" valign="top">std::vector&lt; <a class="el" href="structOpenMS_1_1ParameterInformation.html">ParameterInformation</a> &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TOPPBase.html#a60bdece826d183bdadb31c85126c3431">paramToParameterInformation_</a> (const <a class="el" href="classOpenMS_1_1Param.html">Param</a> &amp;param) const </td></tr>
<tr class="memdesc:a60bdece826d183bdadb31c85126c3431 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="mdescLeft">&#160;</td><td class="mdescRight">Translates the given parameter object into a vector of <a class="el" href="structOpenMS_1_1ParameterInformation.html" title="Struct that captures all information of a command line parameter. ">ParameterInformation</a>, that can be utilized for cl parsing.  <a href="#a60bdece826d183bdadb31c85126c3431">More...</a><br/></td></tr>
<tr class="separator:a60bdece826d183bdadb31c85126c3431 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:aaab74d8a8bd1c289715d37dc53d37e45 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memItemLeft" align="right" valign="top"><a class="el" href="structOpenMS_1_1ParameterInformation.html">ParameterInformation</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TOPPBase.html#aaab74d8a8bd1c289715d37dc53d37e45">paramEntryToParameterInformation_</a> (const <a class="el" href="structOpenMS_1_1Param_1_1ParamEntry.html">Param::ParamEntry</a> &amp;entry, const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;argument=&quot;&quot;, const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;full_name=&quot;&quot;) const </td></tr>
<tr class="memdesc:aaab74d8a8bd1c289715d37dc53d37e45 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="mdescLeft">&#160;</td><td class="mdescRight">Transforms a ParamEntry object to command line parameter (<a class="el" href="structOpenMS_1_1ParameterInformation.html" title="Struct that captures all information of a command line parameter. ">ParameterInformation</a>).  <a href="#aaab74d8a8bd1c289715d37dc53d37e45">More...</a><br/></td></tr>
<tr class="separator:aaab74d8a8bd1c289715d37dc53d37e45 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ac23e82417e25d8621dbd8fd49c32fbb3 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TOPPBase.html#ac23e82417e25d8621dbd8fd49c32fbb3">registerParamSubsectionsAsTOPPSubsections_</a> (const <a class="el" href="classOpenMS_1_1Param.html">Param</a> &amp;param)</td></tr>
<tr class="separator:ac23e82417e25d8621dbd8fd49c32fbb3 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:af53bf0f9b3b7f3832e12461e59bc49e3 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TOPPBase.html#af53bf0f9b3b7f3832e12461e59bc49e3">registerFullParam_</a> (const <a class="el" href="classOpenMS_1_1Param.html">Param</a> &amp;param)</td></tr>
<tr class="memdesc:af53bf0f9b3b7f3832e12461e59bc49e3 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="mdescLeft">&#160;</td><td class="mdescRight">Register command line parameters for all entries in a <a class="el" href="classOpenMS_1_1Param.html" title="Management and storage of parameters / INI files. ">Param</a> object.  <a href="#af53bf0f9b3b7f3832e12461e59bc49e3">More...</a><br/></td></tr>
<tr class="separator:af53bf0f9b3b7f3832e12461e59bc49e3 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:aca68ab170c4b79ce48c84a63f4f7c0a0 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TOPPBase.html#aca68ab170c4b79ce48c84a63f4f7c0a0">registerStringOption_</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;name, const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;argument, const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;default_value, const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;description, bool required=true, bool advanced=false)</td></tr>
<tr class="memdesc:aca68ab170c4b79ce48c84a63f4f7c0a0 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="mdescLeft">&#160;</td><td class="mdescRight">Registers a string option.  <a href="#aca68ab170c4b79ce48c84a63f4f7c0a0">More...</a><br/></td></tr>
<tr class="separator:aca68ab170c4b79ce48c84a63f4f7c0a0 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a85b8cf00b055fed0dca275fa28c87387 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TOPPBase.html#a85b8cf00b055fed0dca275fa28c87387">setValidStrings_</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;name, const std::vector&lt; <a class="el" href="classOpenMS_1_1String.html">String</a> &gt; &amp;strings)</td></tr>
<tr class="memdesc:a85b8cf00b055fed0dca275fa28c87387 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="mdescLeft">&#160;</td><td class="mdescRight">Sets the valid strings for a string option or a whole string list.  <a href="#a85b8cf00b055fed0dca275fa28c87387">More...</a><br/></td></tr>
<tr class="separator:a85b8cf00b055fed0dca275fa28c87387 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a210a0761b8809e09b84f66024b0ee591 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TOPPBase.html#a210a0761b8809e09b84f66024b0ee591">registerInputFile_</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;name, const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;argument, const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;default_value, const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;description, bool required=true, bool advanced=false, const <a class="el" href="classOpenMS_1_1StringList.html">StringList</a> &amp;tags=<a class="el" href="classOpenMS_1_1StringList.html">StringList</a>())</td></tr>
<tr class="memdesc:a210a0761b8809e09b84f66024b0ee591 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="mdescLeft">&#160;</td><td class="mdescRight">Registers an input file option.  <a href="#a210a0761b8809e09b84f66024b0ee591">More...</a><br/></td></tr>
<tr class="separator:a210a0761b8809e09b84f66024b0ee591 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:aa1c190a70c3e51b88bdd71113f061ad8 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TOPPBase.html#aa1c190a70c3e51b88bdd71113f061ad8">registerOutputFile_</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;name, const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;argument, const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;default_value, const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;description, bool required=true, bool advanced=false)</td></tr>
<tr class="memdesc:aa1c190a70c3e51b88bdd71113f061ad8 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="mdescLeft">&#160;</td><td class="mdescRight">Registers an output file option.  <a href="#aa1c190a70c3e51b88bdd71113f061ad8">More...</a><br/></td></tr>
<tr class="separator:aa1c190a70c3e51b88bdd71113f061ad8 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a505102880fe265ea8560ee9136e76fc0 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TOPPBase.html#a505102880fe265ea8560ee9136e76fc0">setValidFormats_</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;name, const std::vector&lt; <a class="el" href="classOpenMS_1_1String.html">String</a> &gt; &amp;formats, const bool force_OpenMS_format=true)</td></tr>
<tr class="memdesc:a505102880fe265ea8560ee9136e76fc0 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="mdescLeft">&#160;</td><td class="mdescRight">Sets the formats for a input/output file option or for all members of an input/output file lists.  <a href="#a505102880fe265ea8560ee9136e76fc0">More...</a><br/></td></tr>
<tr class="separator:a505102880fe265ea8560ee9136e76fc0 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:aa2d8d3bd5482949c57dd814cff386ca4 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TOPPBase.html#aa2d8d3bd5482949c57dd814cff386ca4">registerDoubleOption_</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;name, const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;argument, <a class="el" href="classdouble.html">double</a> default_value, const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;description, bool required=true, bool advanced=false)</td></tr>
<tr class="memdesc:aa2d8d3bd5482949c57dd814cff386ca4 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="mdescLeft">&#160;</td><td class="mdescRight">Registers a double option.  <a href="#aa2d8d3bd5482949c57dd814cff386ca4">More...</a><br/></td></tr>
<tr class="separator:aa2d8d3bd5482949c57dd814cff386ca4 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a50e2ac598a7f0508f871f64082b33422 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TOPPBase.html#a50e2ac598a7f0508f871f64082b33422">setMinInt_</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;name, <a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> min)</td></tr>
<tr class="memdesc:a50e2ac598a7f0508f871f64082b33422 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="mdescLeft">&#160;</td><td class="mdescRight">Sets the minimum value for the integer parameter(can be a list of integers,too) <code>name</code>.  <a href="#a50e2ac598a7f0508f871f64082b33422">More...</a><br/></td></tr>
<tr class="separator:a50e2ac598a7f0508f871f64082b33422 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a605edef60e83ec4fac8e06b9d8c2456b inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TOPPBase.html#a605edef60e83ec4fac8e06b9d8c2456b">setMaxInt_</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;name, <a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> max)</td></tr>
<tr class="memdesc:a605edef60e83ec4fac8e06b9d8c2456b inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="mdescLeft">&#160;</td><td class="mdescRight">Sets the maximum value for the integer parameter(can be a list of integers,too) <code>name</code>.  <a href="#a605edef60e83ec4fac8e06b9d8c2456b">More...</a><br/></td></tr>
<tr class="separator:a605edef60e83ec4fac8e06b9d8c2456b inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a0c572075f31eb74105e0c6208b4aea53 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TOPPBase.html#a0c572075f31eb74105e0c6208b4aea53">setMinFloat_</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;name, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> min)</td></tr>
<tr class="memdesc:a0c572075f31eb74105e0c6208b4aea53 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="mdescLeft">&#160;</td><td class="mdescRight">Sets the minimum value for the floating point parameter(can be a list of floating points,too) <code>name</code>.  <a href="#a0c572075f31eb74105e0c6208b4aea53">More...</a><br/></td></tr>
<tr class="separator:a0c572075f31eb74105e0c6208b4aea53 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:adf95da344ba3f752eba15df253cecdde inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TOPPBase.html#adf95da344ba3f752eba15df253cecdde">setMaxFloat_</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;name, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> max)</td></tr>
<tr class="memdesc:adf95da344ba3f752eba15df253cecdde inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="mdescLeft">&#160;</td><td class="mdescRight">Sets the maximum value for the floating point parameter(can be a list of floating points,too) <code>name</code>.  <a href="#adf95da344ba3f752eba15df253cecdde">More...</a><br/></td></tr>
<tr class="separator:adf95da344ba3f752eba15df253cecdde inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a51fab2e5bbfa80fb2b3f7197b1210d60 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TOPPBase.html#a51fab2e5bbfa80fb2b3f7197b1210d60">registerIntOption_</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;name, const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;argument, <a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> default_value, const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;description, bool required=true, bool advanced=false)</td></tr>
<tr class="memdesc:a51fab2e5bbfa80fb2b3f7197b1210d60 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="mdescLeft">&#160;</td><td class="mdescRight">Registers an integer option.  <a href="#a51fab2e5bbfa80fb2b3f7197b1210d60">More...</a><br/></td></tr>
<tr class="separator:a51fab2e5bbfa80fb2b3f7197b1210d60 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a3868b16da6290a9ebffacb452caaf9fe inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TOPPBase.html#a3868b16da6290a9ebffacb452caaf9fe">registerIntList_</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;name, const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;argument, <a class="el" href="classOpenMS_1_1IntList.html">IntList</a> default_value, const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;description, bool required=true, bool advanced=false)</td></tr>
<tr class="memdesc:a3868b16da6290a9ebffacb452caaf9fe inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="mdescLeft">&#160;</td><td class="mdescRight">Registers a list of integers option.  <a href="#a3868b16da6290a9ebffacb452caaf9fe">More...</a><br/></td></tr>
<tr class="separator:a3868b16da6290a9ebffacb452caaf9fe inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a59979b92485c117611a056662f8e5b3a inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TOPPBase.html#a59979b92485c117611a056662f8e5b3a">registerDoubleList_</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;name, const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;argument, <a class="el" href="classOpenMS_1_1DoubleList.html">DoubleList</a> default_value, const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;description, bool required=true, bool advanced=false)</td></tr>
<tr class="memdesc:a59979b92485c117611a056662f8e5b3a inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="mdescLeft">&#160;</td><td class="mdescRight">Registers a list of doubles option.  <a href="#a59979b92485c117611a056662f8e5b3a">More...</a><br/></td></tr>
<tr class="separator:a59979b92485c117611a056662f8e5b3a inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a32f07daff0e43a1118673be3769239f8 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TOPPBase.html#a32f07daff0e43a1118673be3769239f8">registerStringList_</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;name, const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;argument, <a class="el" href="classOpenMS_1_1StringList.html">StringList</a> default_value, const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;description, bool required=true, bool advanced=false)</td></tr>
<tr class="memdesc:a32f07daff0e43a1118673be3769239f8 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="mdescLeft">&#160;</td><td class="mdescRight">Registers a list of strings option.  <a href="#a32f07daff0e43a1118673be3769239f8">More...</a><br/></td></tr>
<tr class="separator:a32f07daff0e43a1118673be3769239f8 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:aa72f87937c83245e39219a16ae70b58a inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TOPPBase.html#aa72f87937c83245e39219a16ae70b58a">registerInputFileList_</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;name, const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;argument, <a class="el" href="classOpenMS_1_1StringList.html">StringList</a> default_value, const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;description, bool required=true, bool advanced=false)</td></tr>
<tr class="memdesc:aa72f87937c83245e39219a16ae70b58a inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="mdescLeft">&#160;</td><td class="mdescRight">Registers a list of input files option.  <a href="#aa72f87937c83245e39219a16ae70b58a">More...</a><br/></td></tr>
<tr class="separator:aa72f87937c83245e39219a16ae70b58a inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a55756d2c4466dd29f329abe97783fe0e inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TOPPBase.html#a55756d2c4466dd29f329abe97783fe0e">registerOutputFileList_</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;name, const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;argument, <a class="el" href="classOpenMS_1_1StringList.html">StringList</a> default_value, const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;description, bool required=true, bool advanced=false)</td></tr>
<tr class="memdesc:a55756d2c4466dd29f329abe97783fe0e inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="mdescLeft">&#160;</td><td class="mdescRight">Registers a list of output files option.  <a href="#a55756d2c4466dd29f329abe97783fe0e">More...</a><br/></td></tr>
<tr class="separator:a55756d2c4466dd29f329abe97783fe0e inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a601c44fb542d7beecba59c85a3d7366a inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TOPPBase.html#a601c44fb542d7beecba59c85a3d7366a">registerFlag_</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;name, const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;description, bool advanced=false)</td></tr>
<tr class="memdesc:a601c44fb542d7beecba59c85a3d7366a inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="mdescLeft">&#160;</td><td class="mdescRight">Registers a flag.  <a href="#a601c44fb542d7beecba59c85a3d7366a">More...</a><br/></td></tr>
<tr class="separator:a601c44fb542d7beecba59c85a3d7366a inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:af1df3cd0dbce060db3787b38f1a0f5d4 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TOPPBase.html#af1df3cd0dbce060db3787b38f1a0f5d4">registerSubsection_</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;name, const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;description)</td></tr>
<tr class="memdesc:af1df3cd0dbce060db3787b38f1a0f5d4 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="mdescLeft">&#160;</td><td class="mdescRight">Registers an allowed subsection in the INI file (usually from <a class="el" href="namespaceOpenMS.html" title="Main OpenMS namespace. ">OpenMS</a> algorithms).  <a href="#af1df3cd0dbce060db3787b38f1a0f5d4">More...</a><br/></td></tr>
<tr class="separator:af1df3cd0dbce060db3787b38f1a0f5d4 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a458a3005edef7474966e6db4b5aba9ef inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TOPPBase.html#a458a3005edef7474966e6db4b5aba9ef">registerTOPPSubsection_</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;name, const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;description)</td></tr>
<tr class="memdesc:a458a3005edef7474966e6db4b5aba9ef inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="mdescLeft">&#160;</td><td class="mdescRight">Registers an allowed subsection in the INI file originating from the TOPP tool itself.  <a href="#a458a3005edef7474966e6db4b5aba9ef">More...</a><br/></td></tr>
<tr class="separator:a458a3005edef7474966e6db4b5aba9ef inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a16d8261b0f0279c408f75e7470d47cb9 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TOPPBase.html#a16d8261b0f0279c408f75e7470d47cb9">addEmptyLine_</a> ()</td></tr>
<tr class="memdesc:a16d8261b0f0279c408f75e7470d47cb9 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="mdescLeft">&#160;</td><td class="mdescRight">Adds an empty line between registered variables in the documentation.  <a href="#a16d8261b0f0279c408f75e7470d47cb9">More...</a><br/></td></tr>
<tr class="separator:a16d8261b0f0279c408f75e7470d47cb9 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ad0f435ce828122992e3f38ed021707cd inherit pro_methods_classOpenMS_1_1TOPPBase"><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_1TOPPBase.html#ad0f435ce828122992e3f38ed021707cd">getStringOption_</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;name) const </td></tr>
<tr class="memdesc:ad0f435ce828122992e3f38ed021707cd inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="mdescLeft">&#160;</td><td class="mdescRight">Returns the value of a previously registered string option.  <a href="#ad0f435ce828122992e3f38ed021707cd">More...</a><br/></td></tr>
<tr class="separator:ad0f435ce828122992e3f38ed021707cd inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a65d200b37c1378a90b8489187a758f36 inherit pro_methods_classOpenMS_1_1TOPPBase"><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_1TOPPBase.html#a65d200b37c1378a90b8489187a758f36">getDoubleOption_</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;name) const </td></tr>
<tr class="memdesc:a65d200b37c1378a90b8489187a758f36 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="mdescLeft">&#160;</td><td class="mdescRight">Returns the value of a previously registered double option.  <a href="#a65d200b37c1378a90b8489187a758f36">More...</a><br/></td></tr>
<tr class="separator:a65d200b37c1378a90b8489187a758f36 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a46dc9a57f9881913b5d235fbfb1bde6a inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TOPPBase.html#a46dc9a57f9881913b5d235fbfb1bde6a">getIntOption_</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;name) const </td></tr>
<tr class="memdesc:a46dc9a57f9881913b5d235fbfb1bde6a inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="mdescLeft">&#160;</td><td class="mdescRight">Returns the value of a previously registered integer option.  <a href="#a46dc9a57f9881913b5d235fbfb1bde6a">More...</a><br/></td></tr>
<tr class="separator:a46dc9a57f9881913b5d235fbfb1bde6a inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ae7a9bad19f134cd3bc2ea1ebe754edfc inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1StringList.html">StringList</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TOPPBase.html#ae7a9bad19f134cd3bc2ea1ebe754edfc">getStringList_</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;name) const </td></tr>
<tr class="memdesc:ae7a9bad19f134cd3bc2ea1ebe754edfc inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="mdescLeft">&#160;</td><td class="mdescRight">Returns the value of a previously registered <a class="el" href="classOpenMS_1_1StringList.html" title="String list. ">StringList</a>.  <a href="#ae7a9bad19f134cd3bc2ea1ebe754edfc">More...</a><br/></td></tr>
<tr class="separator:ae7a9bad19f134cd3bc2ea1ebe754edfc inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ad5b87a7b41d5b978674a05366cb7a624 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1IntList.html">IntList</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TOPPBase.html#ad5b87a7b41d5b978674a05366cb7a624">getIntList_</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;name) const </td></tr>
<tr class="memdesc:ad5b87a7b41d5b978674a05366cb7a624 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="mdescLeft">&#160;</td><td class="mdescRight">Returns the value of a previously registered <a class="el" href="classOpenMS_1_1IntList.html" title="Int list. ">IntList</a>.  <a href="#ad5b87a7b41d5b978674a05366cb7a624">More...</a><br/></td></tr>
<tr class="separator:ad5b87a7b41d5b978674a05366cb7a624 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ad107e42a148241f171cbf7806d0a1f11 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1DoubleList.html">DoubleList</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TOPPBase.html#ad107e42a148241f171cbf7806d0a1f11">getDoubleList_</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;name) const </td></tr>
<tr class="memdesc:ad107e42a148241f171cbf7806d0a1f11 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="mdescLeft">&#160;</td><td class="mdescRight">Returns the value of a previously registered <a class="el" href="classOpenMS_1_1DoubleList.html" title="DoubleReal list. ">DoubleList</a>.  <a href="#ad107e42a148241f171cbf7806d0a1f11">More...</a><br/></td></tr>
<tr class="separator:ad107e42a148241f171cbf7806d0a1f11 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a561c35c70c82eb02754e469532ef89f1 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TOPPBase.html#a561c35c70c82eb02754e469532ef89f1">getFlag_</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;name) const </td></tr>
<tr class="memdesc:a561c35c70c82eb02754e469532ef89f1 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="mdescLeft">&#160;</td><td class="mdescRight">Returns the value of a previously registered flag.  <a href="#a561c35c70c82eb02754e469532ef89f1">More...</a><br/></td></tr>
<tr class="separator:a561c35c70c82eb02754e469532ef89f1 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ac4f6cb42456ba078653d44e8c8259c2d inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="structOpenMS_1_1ParameterInformation.html">ParameterInformation</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TOPPBase.html#ac4f6cb42456ba078653d44e8c8259c2d">findEntry_</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;name) const </td></tr>
<tr class="memdesc:ac4f6cb42456ba078653d44e8c8259c2d inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="mdescLeft">&#160;</td><td class="mdescRight">Finds the entry in the parameters_ array that has the name <code>name</code>.  <a href="#ac4f6cb42456ba078653d44e8c8259c2d">More...</a><br/></td></tr>
<tr class="separator:ac4f6cb42456ba078653d44e8c8259c2d inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:aed056273aa42c9778f16375e0bffbc86 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1Param.html">Param</a> const &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TOPPBase.html#aed056273aa42c9778f16375e0bffbc86">getParam_</a> () const </td></tr>
<tr class="memdesc:aed056273aa42c9778f16375e0bffbc86 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="mdescLeft">&#160;</td><td class="mdescRight">Return <em>all</em> parameters relevant to this TOPP tool.  <a href="#aed056273aa42c9778f16375e0bffbc86">More...</a><br/></td></tr>
<tr class="separator:aed056273aa42c9778f16375e0bffbc86 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ab27e7a49941fc5131d7bc7cb7f4014d5 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TOPPBase.html#ab27e7a49941fc5131d7bc7cb7f4014d5">checkParam_</a> (const <a class="el" href="classOpenMS_1_1Param.html">Param</a> &amp;param, const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;filename, const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;location) const </td></tr>
<tr class="memdesc:ab27e7a49941fc5131d7bc7cb7f4014d5 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="mdescLeft">&#160;</td><td class="mdescRight">Checks top-level entries of <code>param</code> according to the information during registration.  <a href="#ab27e7a49941fc5131d7bc7cb7f4014d5">More...</a><br/></td></tr>
<tr class="separator:ab27e7a49941fc5131d7bc7cb7f4014d5 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ae08d8cef4a574ae28416e1b7fd82dcd1 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TOPPBase.html#ae08d8cef4a574ae28416e1b7fd82dcd1">checkIfIniParametersAreApplicable_</a> (const <a class="el" href="classOpenMS_1_1Param.html">Param</a> &amp;ini_params)</td></tr>
<tr class="memdesc:ae08d8cef4a574ae28416e1b7fd82dcd1 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="mdescLeft">&#160;</td><td class="mdescRight">Checks if the parameters of the provided ini file are applicable to this tool.  <a href="#ae08d8cef4a574ae28416e1b7fd82dcd1">More...</a><br/></td></tr>
<tr class="separator:ae08d8cef4a574ae28416e1b7fd82dcd1 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ada8464ea991bff8328219140f57f27e2 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TOPPBase.html#ada8464ea991bff8328219140f57f27e2">writeLog_</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;text) const </td></tr>
<tr class="memdesc:ada8464ea991bff8328219140f57f27e2 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="mdescLeft">&#160;</td><td class="mdescRight">Writes a string to the log file and to std::cout.  <a href="#ada8464ea991bff8328219140f57f27e2">More...</a><br/></td></tr>
<tr class="separator:ada8464ea991bff8328219140f57f27e2 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ab0d28c26fe4909b495313dcb6c9adecc inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TOPPBase.html#ab0d28c26fe4909b495313dcb6c9adecc">writeDebug_</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;text, <a class="el" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a> min_level) const </td></tr>
<tr class="memdesc:ab0d28c26fe4909b495313dcb6c9adecc inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="mdescLeft">&#160;</td><td class="mdescRight">Writes a <code>text</code> to the log file and to std::cout if the debug level is at least <code>min_level</code>.  <a href="#ab0d28c26fe4909b495313dcb6c9adecc">More...</a><br/></td></tr>
<tr class="separator:ab0d28c26fe4909b495313dcb6c9adecc inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a1a3e3bbe05fdaad8ea45eaaac44e559e inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TOPPBase.html#a1a3e3bbe05fdaad8ea45eaaac44e559e">writeDebug_</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;text, const <a class="el" href="classOpenMS_1_1Param.html">Param</a> &amp;param, <a class="el" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a> min_level) const </td></tr>
<tr class="memdesc:a1a3e3bbe05fdaad8ea45eaaac44e559e inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="mdescLeft">&#160;</td><td class="mdescRight">Writes a <a class="el" href="classOpenMS_1_1String.html" title="A more convenient string class. ">String</a> followed by a <a class="el" href="classOpenMS_1_1Param.html" title="Management and storage of parameters / INI files. ">Param</a> to the log file and to std::cout if the debug level is at least <code>min_level</code>.  <a href="#a1a3e3bbe05fdaad8ea45eaaac44e559e">More...</a><br/></td></tr>
<tr class="separator:a1a3e3bbe05fdaad8ea45eaaac44e559e inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a1763ff9f1c0dd1169564a9c8b12138e2 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TOPPBase.html#a1763ff9f1c0dd1169564a9c8b12138e2">inputFileReadable_</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;filename, const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;param_name) const </td></tr>
<tr class="memdesc:a1763ff9f1c0dd1169564a9c8b12138e2 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="mdescLeft">&#160;</td><td class="mdescRight">Checks if an input file exists, is readable and is not empty.  <a href="#a1763ff9f1c0dd1169564a9c8b12138e2">More...</a><br/></td></tr>
<tr class="separator:a1763ff9f1c0dd1169564a9c8b12138e2 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ab0566c8904244b97a929edb047cccb3c inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TOPPBase.html#ab0566c8904244b97a929edb047cccb3c">outputFileWritable_</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;filename, const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;param_name) const </td></tr>
<tr class="memdesc:ab0566c8904244b97a929edb047cccb3c inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="mdescLeft">&#160;</td><td class="mdescRight">Checks if an output file is writeable.  <a href="#ab0566c8904244b97a929edb047cccb3c">More...</a><br/></td></tr>
<tr class="separator:ab0566c8904244b97a929edb047cccb3c inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a1254afd939487eab144c794a247fca86 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TOPPBase.html#a1254afd939487eab144c794a247fca86">addDataProcessing_</a> (<a class="el" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a> &amp;map, const <a class="el" href="classOpenMS_1_1DataProcessing.html">DataProcessing</a> &amp;dp) const </td></tr>
<tr class="memdesc:a1254afd939487eab144c794a247fca86 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="mdescLeft">&#160;</td><td class="mdescRight">Data processing setter for consensus maps.  <a href="#a1254afd939487eab144c794a247fca86">More...</a><br/></td></tr>
<tr class="separator:a1254afd939487eab144c794a247fca86 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a4ba03f6d26e49c1834ad8acf13a7b0a0 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memTemplParams" colspan="2">template&lt;typename FeatureType &gt; </td></tr>
<tr class="memitem:a4ba03f6d26e49c1834ad8acf13a7b0a0 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memTemplItemLeft" align="right" valign="top">void&#160;</td><td class="memTemplItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TOPPBase.html#a4ba03f6d26e49c1834ad8acf13a7b0a0">addDataProcessing_</a> (<a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a>&lt; FeatureType &gt; &amp;map, const <a class="el" href="classOpenMS_1_1DataProcessing.html">DataProcessing</a> &amp;dp) const </td></tr>
<tr class="memdesc:a4ba03f6d26e49c1834ad8acf13a7b0a0 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="mdescLeft">&#160;</td><td class="mdescRight">Data processing setter for feature maps.  <a href="#a4ba03f6d26e49c1834ad8acf13a7b0a0">More...</a><br/></td></tr>
<tr class="separator:a4ba03f6d26e49c1834ad8acf13a7b0a0 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a8e50b81e2c3372c6c9529b10e6f1bf80 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memTemplParams" colspan="2">template&lt;typename PeakType , typename CT &gt; </td></tr>
<tr class="memitem:a8e50b81e2c3372c6c9529b10e6f1bf80 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memTemplItemLeft" align="right" valign="top">void&#160;</td><td class="memTemplItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TOPPBase.html#a8e50b81e2c3372c6c9529b10e6f1bf80">addDataProcessing_</a> (<a class="el" href="classOpenMS_1_1MSExperiment.html">MSExperiment</a>&lt; <a class="el" href="namespaceOpenMS.html#a013338b7bdbb5c3b4c78666656070e23">PeakType</a>, CT &gt; &amp;map, const <a class="el" href="classOpenMS_1_1DataProcessing.html">DataProcessing</a> &amp;dp) const </td></tr>
<tr class="memdesc:a8e50b81e2c3372c6c9529b10e6f1bf80 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="mdescLeft">&#160;</td><td class="mdescRight">Data processing setter for peak maps.  <a href="#a8e50b81e2c3372c6c9529b10e6f1bf80">More...</a><br/></td></tr>
<tr class="separator:a8e50b81e2c3372c6c9529b10e6f1bf80 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ae5d4d42b1f3c15788ce474275691f2f7 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1DataProcessing.html">DataProcessing</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TOPPBase.html#ae5d4d42b1f3c15788ce474275691f2f7">getProcessingInfo_</a> (<a class="el" href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9">DataProcessing::ProcessingAction</a> action) const </td></tr>
<tr class="memdesc:ae5d4d42b1f3c15788ce474275691f2f7 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="mdescLeft">&#160;</td><td class="mdescRight">Returns the the data processing information.  <a href="#ae5d4d42b1f3c15788ce474275691f2f7">More...</a><br/></td></tr>
<tr class="separator:ae5d4d42b1f3c15788ce474275691f2f7 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ad8980143803456722905c79a0110fab6 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1DataProcessing.html">DataProcessing</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TOPPBase.html#ad8980143803456722905c79a0110fab6">getProcessingInfo_</a> (const std::set&lt; <a class="el" href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9">DataProcessing::ProcessingAction</a> &gt; &amp;actions) const </td></tr>
<tr class="memdesc:ad8980143803456722905c79a0110fab6 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="mdescLeft">&#160;</td><td class="mdescRight">Returns the the data processing information.  <a href="#ad8980143803456722905c79a0110fab6">More...</a><br/></td></tr>
<tr class="separator:ad8980143803456722905c79a0110fab6 inherit pro_methods_classOpenMS_1_1TOPPBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="inherited"></a>
Additional Inherited Members</h2></td></tr>
<tr class="inherit_header pub_types_classOpenMS_1_1TOPPBase"><td colspan="2" onclick="javascript:toggleInherit('pub_types_classOpenMS_1_1TOPPBase')"><img src="closed.png" alt="-"/>&#160;Public Types inherited from <a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td></tr>
<tr class="memitem:ac74ddc700cf9fcf91d688b6d31ff9537 inherit pub_types_classOpenMS_1_1TOPPBase"><td class="memItemLeft" align="right" valign="top">enum &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537">ExitCodes</a> { <br/>
&#160;&#160;<a class="el" href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537a88fa85c1c9370642a3ca9276d6fcff7c">EXECUTION_OK</a>, 
<a class="el" href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537aa7f4f2e83db4048bd7e4190a53c3fd1a">INPUT_FILE_NOT_FOUND</a>, 
<a class="el" href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537aaceec1bc6fad40534fb0a9e187ce598e">INPUT_FILE_NOT_READABLE</a>, 
<a class="el" href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537a18661839b1b50ff3c7f13344f1b9dc2b">INPUT_FILE_CORRUPT</a>, 
<br/>
&#160;&#160;<a class="el" href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537a10df6a9738d612d102fe7ef636be66ee">INPUT_FILE_EMPTY</a>, 
<a class="el" href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537ac1cb71a829967f44c382c253fdf2d90b">CANNOT_WRITE_OUTPUT_FILE</a>, 
<a class="el" href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537a387a807fbe7719a9e3862b4d72282305">ILLEGAL_PARAMETERS</a>, 
<a class="el" href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537a3ff91cf9f0ce3066dfb408d97fbe81ff">MISSING_PARAMETERS</a>, 
<br/>
&#160;&#160;<a class="el" href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537a8216aa4b3a817cdf8c15ed32aa946e83">UNKNOWN_ERROR</a>, 
<a class="el" href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537a56a605c1df1029022a47df8a5fe57c5a">EXTERNAL_PROGRAM_ERROR</a>, 
<a class="el" href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537ad73f40ad2eef48a6ca24988909c66c3e">PARSE_ERROR</a>, 
<a class="el" href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537a61cd58829fafa9611e98b767acc3a0a5">INCOMPATIBLE_INPUT_DATA</a>, 
<br/>
&#160;&#160;<a class="el" href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537aa6160da3d147c897d800efe3a69c941e">INTERNAL_ERROR</a>, 
<a class="el" href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537ae379f86cc4ef6f5ad8eb2b414772bc0a">UNEXPECTED_RESULT</a>
<br/>
 }</td></tr>
<tr class="memdesc:ac74ddc700cf9fcf91d688b6d31ff9537"><td class="mdescLeft">&#160;</td><td class="mdescRight">Exit codes.  <a href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537">More...</a><br/></td></tr>
<tr class="separator:ac74ddc700cf9fcf91d688b6d31ff9537 inherit pub_types_classOpenMS_1_1TOPPBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="inherit_header pub_static_methods_classOpenMS_1_1TOPPBase"><td colspan="2" onclick="javascript:toggleInherit('pub_static_methods_classOpenMS_1_1TOPPBase')"><img src="closed.png" alt="-"/>&#160;Static Public Member Functions inherited from <a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td></tr>
<tr class="memitem:abb40d991085e7c611f6c96de6c45ddb9 inherit pub_static_methods_classOpenMS_1_1TOPPBase"><td class="memItemLeft" align="right" valign="top">static void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TOPPBase.html#abb40d991085e7c611f6c96de6c45ddb9">setMaxNumberOfThreads</a> (int num_threads)</td></tr>
<tr class="memdesc:abb40d991085e7c611f6c96de6c45ddb9 inherit pub_static_methods_classOpenMS_1_1TOPPBase"><td class="mdescLeft">&#160;</td><td class="mdescRight">Sets the maximal number of usable threads.  <a href="#abb40d991085e7c611f6c96de6c45ddb9">More...</a><br/></td></tr>
<tr class="separator:abb40d991085e7c611f6c96de6c45ddb9 inherit pub_static_methods_classOpenMS_1_1TOPPBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="inherit_header pro_attribs_classOpenMS_1_1TOPPBase"><td colspan="2" onclick="javascript:toggleInherit('pro_attribs_classOpenMS_1_1TOPPBase')"><img src="closed.png" alt="-"/>&#160;Protected Attributes inherited from <a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td></tr>
<tr class="memitem:a4e87a8f69bbc06cd56776556dc1680ed inherit pro_attribs_classOpenMS_1_1TOPPBase"><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_1TOPPBase.html#a4e87a8f69bbc06cd56776556dc1680ed">version_</a></td></tr>
<tr class="memdesc:a4e87a8f69bbc06cd56776556dc1680ed inherit pro_attribs_classOpenMS_1_1TOPPBase"><td class="mdescLeft">&#160;</td><td class="mdescRight">Version string (if empty, the OpenMS/TOPP version is printed)  <a href="#a4e87a8f69bbc06cd56776556dc1680ed">More...</a><br/></td></tr>
<tr class="separator:a4e87a8f69bbc06cd56776556dc1680ed inherit pro_attribs_classOpenMS_1_1TOPPBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a65de5468e578e72bc9fe6f4e603a29b3 inherit pro_attribs_classOpenMS_1_1TOPPBase"><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_1TOPPBase.html#a65de5468e578e72bc9fe6f4e603a29b3">verboseVersion_</a></td></tr>
<tr class="memdesc:a65de5468e578e72bc9fe6f4e603a29b3 inherit pro_attribs_classOpenMS_1_1TOPPBase"><td class="mdescLeft">&#160;</td><td class="mdescRight">Version string including additional revision/date time information. Note: This differs from version_ only if not provided by the user.  <a href="#a65de5468e578e72bc9fe6f4e603a29b3">More...</a><br/></td></tr>
<tr class="separator:a65de5468e578e72bc9fe6f4e603a29b3 inherit pro_attribs_classOpenMS_1_1TOPPBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a980b56a8b0110ffe7e3cda4060b3f289 inherit pro_attribs_classOpenMS_1_1TOPPBase"><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TOPPBase.html#a980b56a8b0110ffe7e3cda4060b3f289">official_</a></td></tr>
<tr class="memdesc:a980b56a8b0110ffe7e3cda4060b3f289 inherit pro_attribs_classOpenMS_1_1TOPPBase"><td class="mdescLeft">&#160;</td><td class="mdescRight">Flag indicating if this an official TOPP tool.  <a href="#a980b56a8b0110ffe7e3cda4060b3f289">More...</a><br/></td></tr>
<tr class="separator:a980b56a8b0110ffe7e3cda4060b3f289 inherit pro_attribs_classOpenMS_1_1TOPPBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a5a41e046ecca99c99103faa7214118ee inherit pro_attribs_classOpenMS_1_1TOPPBase"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87c">ProgressLogger::LogType</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TOPPBase.html#a5a41e046ecca99c99103faa7214118ee">log_type_</a></td></tr>
<tr class="memdesc:a5a41e046ecca99c99103faa7214118ee inherit pro_attribs_classOpenMS_1_1TOPPBase"><td class="mdescLeft">&#160;</td><td class="mdescRight">Type of progress logging.  <a href="#a5a41e046ecca99c99103faa7214118ee">More...</a><br/></td></tr>
<tr class="separator:a5a41e046ecca99c99103faa7214118ee inherit pro_attribs_classOpenMS_1_1TOPPBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a6e61791b6ff20c4e71142b700b0ad79a inherit pro_attribs_classOpenMS_1_1TOPPBase"><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TOPPBase.html#a6e61791b6ff20c4e71142b700b0ad79a">test_mode_</a></td></tr>
<tr class="memdesc:a6e61791b6ff20c4e71142b700b0ad79a inherit pro_attribs_classOpenMS_1_1TOPPBase"><td class="mdescLeft">&#160;</td><td class="mdescRight">Test mode.  <a href="#a6e61791b6ff20c4e71142b700b0ad79a">More...</a><br/></td></tr>
<tr class="separator:a6e61791b6ff20c4e71142b700b0ad79a inherit pro_attribs_classOpenMS_1_1TOPPBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a92afa13732182773146571769799a6e3 inherit pro_attribs_classOpenMS_1_1TOPPBase"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TOPPBase.html#a92afa13732182773146571769799a6e3">debug_level_</a></td></tr>
<tr class="memdesc:a92afa13732182773146571769799a6e3 inherit pro_attribs_classOpenMS_1_1TOPPBase"><td class="mdescLeft">&#160;</td><td class="mdescRight">Debug level set by -debug.  <a href="#a92afa13732182773146571769799a6e3">More...</a><br/></td></tr>
<tr class="separator:a92afa13732182773146571769799a6e3 inherit pro_attribs_classOpenMS_1_1TOPPBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="inherit_header pro_static_attribs_classOpenMS_1_1TOPPBase"><td colspan="2" onclick="javascript:toggleInherit('pro_static_attribs_classOpenMS_1_1TOPPBase')"><img src="closed.png" alt="-"/>&#160;Static Protected Attributes inherited from <a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td></tr>
<tr class="memitem:a3857c6970f5c49182a97916a1aa2d555 inherit pro_static_attribs_classOpenMS_1_1TOPPBase"><td class="memItemLeft" align="right" valign="top">static <a class="el" href="classOpenMS_1_1String.html">String</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TOPPBase.html#a3857c6970f5c49182a97916a1aa2d555">topp_ini_file_</a></td></tr>
<tr class="memdesc:a3857c6970f5c49182a97916a1aa2d555 inherit pro_static_attribs_classOpenMS_1_1TOPPBase"><td class="mdescLeft">&#160;</td><td class="mdescRight">.TOPP.ini file for storing system default parameters  <a href="#a3857c6970f5c49182a97916a1aa2d555">More...</a><br/></td></tr>
<tr class="separator:a3857c6970f5c49182a97916a1aa2d555 inherit pro_static_attribs_classOpenMS_1_1TOPPBase"><td class="memSeparator" colspan="2">&#160;</td></tr>
</table>
<h2 class="groupheader">Constructor &amp; Destructor Documentation</h2>
<a class="anchor" id="abf14ac0ef5097d17e6a377ae89b31772"></a>
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      <table class="memname">
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          <td class="memname"><a class="el" href="classTOPPRNPxl.html">TOPPRNPxl</a> </td>
          <td>(</td>
          <td class="paramname"></td><td>)</td>
          <td></td>
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      </table>
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  <td class="mlabels-right">
<span class="mlabels"><span class="mlabel">inline</span></span>  </td>
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</div><div class="memdoc">

</div>
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<h2 class="groupheader">Member Function Documentation</h2>
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          <td class="memname"><a class="el" href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537">ExitCodes</a> main_ </td>
          <td>(</td>
          <td class="paramtype">int&#160;</td>
          <td class="paramname"><em>argc</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">const char **&#160;</td>
          <td class="paramname"><em>argv</em>&#160;</td>
        </tr>
        <tr>
          <td></td>
          <td>)</td>
          <td></td><td></td>
        </tr>
      </table>
  </td>
  <td class="mlabels-right">
<span class="mlabels"><span class="mlabel">inline</span><span class="mlabel">protected</span><span class="mlabel">virtual</span></span>  </td>
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<p>The actual "main" method. <a class="el" href="classTOPPRNPxl.html#ae6668492d67ea303296f9db6ac56325c" title="The actual &quot;main&quot; method. main_() is invoked by main(). ">main_()</a> is invoked by <a class="el" href="classOpenMS_1_1TOPPBase.html#a6f464153a13b38c04f41b4ec9d9714c5" title="Main routine of all TOPP applications. ">main()</a>. </p>

<p>Implements <a class="el" href="classOpenMS_1_1TOPPBase.html#acc240728b4a31cfd01ccfa5aa1490263">TOPPBase</a>.</p>

<p>References <a class="el" href="classOpenMS_1_1MSExperiment.html#ae9dafbb74a1a4c430ceef03e25ab8e10">MSExperiment&lt; PeakT, ChromatogramPeakT &gt;::addSpectrum()</a>, <a class="el" href="classOpenMS_1_1PeptideIdentification.html#aa79958ac1cf2cb1fc4b9ae1cd766cfcb">PeptideIdentification::assignRanks()</a>, <a class="el" href="classOpenMS_1_1MSExperiment.html#a2387033802383edbdc95f9bbb12a707e">MSExperiment&lt; PeakT, ChromatogramPeakT &gt;::begin()</a>, <a class="el" href="classOpenMS_1_1MSExperiment.html#ab45dae688fc5d8983727abffa4389003">MSExperiment&lt; PeakT, ChromatogramPeakT &gt;::end()</a>, <a class="el" href="structMarkerIonExtractor.html#a322f00d683679b32e4f51037bf3a5f70">MarkerIonExtractor::extractMarkerIons()</a>, <a class="el" href="classOpenMS_1_1PeptideIdentification.html#a564d2725cd06914a922d6fbda8be8a13">PeptideIdentification::getHits()</a>, <a class="el" href="classOpenMS_1_1EmpiricalFormula.html#a099406415a8f92305976a24072f6ae84">EmpiricalFormula::getMonoWeight()</a>, <a class="el" href="classOpenMS_1_1MSSpectrum.html#a3da529bd3240fa0d7148484bbef0b9d7">MSSpectrum&lt; PeakT &gt;::getRT()</a>, <a class="el" href="structRNPxlReportRowHeader.html#a75609b7ea482f60c540b56ae3675cbf6">RNPxlReportRowHeader::getString()</a>, <a class="el" href="classOpenMS_1_1String.html#a58599d37159ebc08a654fb2d25be92fe">String::has()</a>, <a class="el" href="RNPxl_8C.html#aacf424b60596dc7e379a9365191f4fd5">initModificationMassesRNA()</a>, <a class="el" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">OpenMS::Constants::k</a>, <a class="el" href="classOpenMS_1_1IdXMLFile.html#a914edf92cb5c95df15eab679bf67691a">IdXMLFile::load()</a>, <a class="el" href="classOpenMS_1_1MzMLFile.html#aed378b9a389ec00fa2b559bf7d3b710b">MzMLFile::load()</a>, <a class="el" href="structModificationMassesResult.html#a3abbaf63406e129003709dde4ff17815">ModificationMassesResult::mod_combinations</a>, <a class="el" href="structModificationMassesResult.html#a2e449c35d50afb3dfd076c78720fb2af">ModificationMassesResult::mod_formula_idx</a>, <a class="el" href="structModificationMassesResult.html#a693ea677ba8f9b3b232b9f9324e18b05">ModificationMassesResult::mod_masses</a>, <a class="el" href="structRNPxlReportRow.html#a1c6732917d0615368e98b9e33577973c">RNPxlReportRow::no_id</a>, <a class="el" href="namespaceOpenMS_1_1Constants.html#a7a25c5ed4c5f83b23ded7014aef42ad4">OpenMS::Constants::PROTON_MASS_U</a>, <a class="el" href="RNPxl_8C.html#acb32bd754908d0f4d1593dbc1941046f">RT_FACTOR</a>, <a class="el" href="RNPxl_8C.html#afdaef593be4273884659462f332c87b6">RT_FACTOR_PRECISION</a>, <a class="el" href="RNPxl_8C.html#aed650f4c2ba2f92aa7f5f5c7a0f1b01f">RT_MODULO_FACTOR</a>, <a class="el" href="classOpenMS_1_1Precursor.html#aca40a4630f5f8a0568899b74a62dcd4b">Precursor::setCharge()</a>, <a class="el" href="classOpenMS_1_1SpectrumSettings.html#a2116f9b1dde8ba3aef4a07e6f2a970a7">SpectrumSettings::setComment()</a>, <a class="el" href="classOpenMS_1_1PeptideIdentification.html#a98447dc4641b69db36fcc5087cfe73e6">PeptideIdentification::setHigherScoreBetter()</a>, <a class="el" href="classOpenMS_1_1PeptideIdentification.html#ab4d15b02dbc53727d0b6dae927ad6688">PeptideIdentification::setHits()</a>, <a class="el" href="classOpenMS_1_1MetaInfoInterface.html#a135a7e818125b31198a8a65d9ac7a3d1">MetaInfoInterface::setMetaValue()</a>, <a class="el" href="classOpenMS_1_1Peak1D.html#ab9c4ce5d172a75d6de2c6f5f1847c9ab">Peak1D::setMZ()</a>, <a class="el" href="classOpenMS_1_1MSSpectrum.html#a77d37f2e1c12e8bd33ea0e660a89e927">MSSpectrum&lt; PeakT &gt;::setName()</a>, <a class="el" href="classOpenMS_1_1SpectrumSettings.html#ad85e4e6fe1ec77097d9108f38a8e57ae">SpectrumSettings::setPrecursors()</a>, <a class="el" href="classOpenMS_1_1MSSpectrum.html#aac8c50f318154e9e5b7b01aee806e17f">MSSpectrum&lt; PeakT &gt;::setRT()</a>, <a class="el" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">MSExperiment&lt; PeakT, ChromatogramPeakT &gt;::size()</a>, <a class="el" href="classOpenMS_1_1IdXMLFile.html#abb7d96da3e275c1d090fc6db3185becd">IdXMLFile::store()</a>, <a class="el" href="classOpenMS_1_1MzMLFile.html#adb795d215478320be7c6130ff7ddf853">MzMLFile::store()</a>, <a class="el" href="classOpenMS_1_1String.html#a8fca08235a25819cf09375f867815f09">String::substitute()</a>, <a class="el" href="classOpenMS_1_1String.html#ab9244483ff324b0dbd3e89d03ee63eb2">String::toQString()</a>, and <a class="el" href="classOpenMS_1_1DataValue.html#abc5a85a6a61fb96964c186b0bf03e1de">DataValue::valueType()</a>.</p>

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          <td class="memname">void registerOptionsAndFlags_ </td>
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<p>Sets the valid command line options (with argument) and flags (without argument). </p>
<p>The options '-ini' '-log' '-instance' '-debug' and the flag '&ndash;help' are automatically registered. </p>

<p>Implements <a class="el" href="classOpenMS_1_1TOPPBase.html#a888a45e3555121aaa36d73032df12a9c">TOPPBase</a>.</p>

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<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:25 using doxygen 1.8.5</font></TD>
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