File: classOpenMS_1_1TOPPBase-members.html

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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_1TOPPBase.html">TOPPBase</a></li>  </ul>
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<p>This is the complete list of members for <a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a>, including all inherited members.</p>
<table class="directory">
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#a1254afd939487eab144c794a247fca86">addDataProcessing_</a>(ConsensusMap &amp;map, const DataProcessing &amp;dp) const </td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#a4ba03f6d26e49c1834ad8acf13a7b0a0">addDataProcessing_</a>(FeatureMap&lt; FeatureType &gt; &amp;map, const DataProcessing &amp;dp) const </td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#a8e50b81e2c3372c6c9529b10e6f1bf80">addDataProcessing_</a>(MSExperiment&lt; PeakType, CT &gt; &amp;map, const DataProcessing &amp;dp) const </td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#a16d8261b0f0279c408f75e7470d47cb9">addEmptyLine_</a>()</td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#a651cd858906ccd50871da7dbba6d4f67">addText_</a>(const String &amp;text)</td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537ac1cb71a829967f44c382c253fdf2d90b">CANNOT_WRITE_OUTPUT_FILE</a> enum value</td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#ae08d8cef4a574ae28416e1b7fd82dcd1">checkIfIniParametersAreApplicable_</a>(const Param &amp;ini_params)</td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#ab27e7a49941fc5131d7bc7cb7f4014d5">checkParam_</a>(const Param &amp;param, const String &amp;filename, const String &amp;location) const </td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#a92afa13732182773146571769799a6e3">debug_level_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#a943ef6026c6d0fab7aa182d1d00e6851">enableLogging_</a>() const </td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537a88fa85c1c9370642a3ca9276d6fcff7c">EXECUTION_OK</a> enum value</td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537">ExitCodes</a> enum name</td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537a56a605c1df1029022a47df8a5fe57c5a">EXTERNAL_PROGRAM_ERROR</a> enum value</td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#ac4f6cb42456ba078653d44e8c8259c2d">findEntry_</a>(const String &amp;name) const </td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#ab5a7f4f8296d7532ea9b9a2b4f9466da">getDefaultParameters_</a>() const </td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#a51bd3e8ab55a00704b0096e417772a02">getDocumentIDTagger_</a>() const </td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#ad107e42a148241f171cbf7806d0a1f11">getDoubleList_</a>(const String &amp;name) const </td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#a65d200b37c1378a90b8489187a758f36">getDoubleOption_</a>(const String &amp;name) const </td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#a561c35c70c82eb02754e469532ef89f1">getFlag_</a>(const String &amp;name) const </td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#ab281176746eb5f3e1ff6441353f0c468">getIniLocation_</a>() const </td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#ad5b87a7b41d5b978674a05366cb7a624">getIntList_</a>(const String &amp;name) const </td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#a46dc9a57f9881913b5d235fbfb1bde6a">getIntOption_</a>(const String &amp;name) const </td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#a0b646c1a8bc3fa87bafedb8c873aea0d">getParam_</a>(const String &amp;key) const </td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#aed056273aa42c9778f16375e0bffbc86">getParam_</a>() const </td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#a094f775e91502e30b2acd25d6434f019">getParamArgument_</a>(const Param::ParamEntry &amp;entry) const </td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#a08daffe2eaee4999730735b9fcbfabf4">getParamAsBool_</a>(const String &amp;key) const </td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#a5b1485d8c3dd02998c757b367bd5b7b8">getParamAsDouble_</a>(const String &amp;key, DoubleReal default_value=0) const </td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#a9c313623474d132d8a973b409a09ab15">getParamAsDoubleList_</a>(const String &amp;key, const DoubleList &amp;default_value) const </td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#aa21cc2fef2758aaee229af63d9d51fdd">getParamAsInt_</a>(const String &amp;key, Int default_value=0) const </td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#a205980c61ed048245360d25628c9c859">getParamAsIntList_</a>(const String &amp;key, const IntList &amp;default_value) const </td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#a02290a3238b0b1218fdf5c44e9e833bf">getParamAsString_</a>(const String &amp;key, const String &amp;default_value=&quot;&quot;) const </td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#a00130f25c821fc7dfbdb0c74166fa4d1">getParamAsStringList_</a>(const String &amp;key, const StringList &amp;default_value) const </td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#af9e884621c0a6fcec24d32ca2999fa97">getParameterByName_</a>(const String &amp;name)</td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#ae5d4d42b1f3c15788ce474275691f2f7">getProcessingInfo_</a>(DataProcessing::ProcessingAction action) const </td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#ad8980143803456722905c79a0110fab6">getProcessingInfo_</a>(const std::set&lt; DataProcessing::ProcessingAction &gt; &amp;actions) const </td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#ae7a9bad19f134cd3bc2ea1ebe754edfc">getStringList_</a>(const String &amp;name) const </td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#ad0f435ce828122992e3f38ed021707cd">getStringOption_</a>(const String &amp;name) const </td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#ab3e424959e7854422a1dd17ae15a9d73">getSubsection_</a>(const String &amp;name) const </td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#aa0b2241d3ddb5e6e4ffab8103efe269f">getSubsectionDefaults_</a>(const String &amp;section) const </td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">private</span><span class="mlabel">virtual</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#a9c770b64a903adc886939cb9fd5648c0">getSubsectionDefaults_</a>() const </td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#acfaf4abf74d839d1e2b915ef77b5c58f">getToolUserDefaults_</a>(const String &amp;tool_name) const </td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#aca70a0389ab53706a919f2df59c343cf">id_tag_support_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#a9cd430d26f556c2dfcf00d07fe5bc89a">id_tagger_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537a387a807fbe7719a9e3862b4d72282305">ILLEGAL_PARAMETERS</a> enum value</td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537a61cd58829fafa9611e98b767acc3a0a5">INCOMPATIBLE_INPUT_DATA</a> enum value</td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#a0978c0a12989743f76ff4ed8073ffdbc">ini_location_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537a18661839b1b50ff3c7f13344f1b9dc2b">INPUT_FILE_CORRUPT</a> enum value</td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537a10df6a9738d612d102fe7ef636be66ee">INPUT_FILE_EMPTY</a> enum value</td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537aa7f4f2e83db4048bd7e4190a53c3fd1a">INPUT_FILE_NOT_FOUND</a> enum value</td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537aaceec1bc6fad40534fb0a9e187ce598e">INPUT_FILE_NOT_READABLE</a> enum value</td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#a1763ff9f1c0dd1169564a9c8b12138e2">inputFileReadable_</a>(const String &amp;filename, const String &amp;param_name) const </td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#a504604d8e42f0ff2cbb9cfac29af2913">instance_number_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537aa6160da3d147c897d800efe3a69c941e">INTERNAL_ERROR</a> enum value</td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#a1fd714af1f19177741eb0b4f6eb43e35">log_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">mutable</span><span class="mlabel">private</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#a5a41e046ecca99c99103faa7214118ee">log_type_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#a6f464153a13b38c04f41b4ec9d9714c5">main</a>(int argc, const char **argv)</td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#acc240728b4a31cfd01ccfa5aa1490263">main_</a>(int argc, const char **argv)=0</td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">protected</span><span class="mlabel">pure virtual</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537a3ff91cf9f0ce3066dfb408d97fbe81ff">MISSING_PARAMETERS</a> enum value</td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#a980b56a8b0110ffe7e3cda4060b3f289">official_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#ab0566c8904244b97a929edb047cccb3c">outputFileWritable_</a>(const String &amp;filename, const String &amp;param_name) const </td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#aa3c6eb7ecbdfa635c6bfcc16beb44abe">param_cmdline_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#afa913f3c5495a38dd42c7f329d94753f">param_common_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#a8d4d920a1b6f34b180feaa33a4a3b204">param_common_tool_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#a055bff6c3f219da094965760ab650fb6">param_inifile_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#a4fa1b8a5454d97f09daeaebca7c91f2e">param_instance_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#aaab74d8a8bd1c289715d37dc53d37e45">paramEntryToParameterInformation_</a>(const Param::ParamEntry &amp;entry, const String &amp;argument=&quot;&quot;, const String &amp;full_name=&quot;&quot;) const </td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#a3935296a9fde5712d711d2fc1100435f">parameters_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#a60bdece826d183bdadb31c85126c3431">paramToParameterInformation_</a>(const Param &amp;param) const </td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537ad73f40ad2eef48a6ca24988909c66c3e">PARSE_ERROR</a> enum value</td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#a3e3d48a52e89fbaa72348f99c3a24295">parseCommandLine_</a>(const int argc, const char **argv, const String &amp;misc=&quot;misc&quot;, const String &amp;unknown=&quot;unknown&quot;)</td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#a598f835681c78f5092d4e6603b783cd8">parseRange_</a>(const String &amp;text, double &amp;low, double &amp;high) const </td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#ac7f9f64984349818c53c9c7b112ba989">parseRange_</a>(const String &amp;text, Int &amp;low, Int &amp;high) const </td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#a48067d9b286e137c0e1a5e7a5ce3ebfc">printUsage_</a>()</td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#a59979b92485c117611a056662f8e5b3a">registerDoubleList_</a>(const String &amp;name, const String &amp;argument, DoubleList default_value, const String &amp;description, bool required=true, bool advanced=false)</td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#aa2d8d3bd5482949c57dd814cff386ca4">registerDoubleOption_</a>(const String &amp;name, const String &amp;argument, double default_value, const String &amp;description, bool required=true, bool advanced=false)</td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#a601c44fb542d7beecba59c85a3d7366a">registerFlag_</a>(const String &amp;name, const String &amp;description, bool advanced=false)</td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#af53bf0f9b3b7f3832e12461e59bc49e3">registerFullParam_</a>(const Param &amp;param)</td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#a210a0761b8809e09b84f66024b0ee591">registerInputFile_</a>(const String &amp;name, const String &amp;argument, const String &amp;default_value, const String &amp;description, bool required=true, bool advanced=false, const StringList &amp;tags=StringList())</td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#aa72f87937c83245e39219a16ae70b58a">registerInputFileList_</a>(const String &amp;name, const String &amp;argument, StringList default_value, const String &amp;description, bool required=true, bool advanced=false)</td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#a3868b16da6290a9ebffacb452caaf9fe">registerIntList_</a>(const String &amp;name, const String &amp;argument, IntList default_value, const String &amp;description, bool required=true, bool advanced=false)</td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#a51fab2e5bbfa80fb2b3f7197b1210d60">registerIntOption_</a>(const String &amp;name, const String &amp;argument, Int default_value, const String &amp;description, bool required=true, bool advanced=false)</td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#a888a45e3555121aaa36d73032df12a9c">registerOptionsAndFlags_</a>()=0</td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">protected</span><span class="mlabel">pure virtual</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#aa1c190a70c3e51b88bdd71113f061ad8">registerOutputFile_</a>(const String &amp;name, const String &amp;argument, const String &amp;default_value, const String &amp;description, bool required=true, bool advanced=false)</td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#a55756d2c4466dd29f329abe97783fe0e">registerOutputFileList_</a>(const String &amp;name, const String &amp;argument, StringList default_value, const String &amp;description, bool required=true, bool advanced=false)</td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#ac23e82417e25d8621dbd8fd49c32fbb3">registerParamSubsectionsAsTOPPSubsections_</a>(const Param &amp;param)</td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#a32f07daff0e43a1118673be3769239f8">registerStringList_</a>(const String &amp;name, const String &amp;argument, StringList default_value, const String &amp;description, bool required=true, bool advanced=false)</td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#aca68ab170c4b79ce48c84a63f4f7c0a0">registerStringOption_</a>(const String &amp;name, const String &amp;argument, const String &amp;default_value, const String &amp;description, bool required=true, bool advanced=false)</td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#af1df3cd0dbce060db3787b38f1a0f5d4">registerSubsection_</a>(const String &amp;name, const String &amp;description)</td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#a458a3005edef7474966e6db4b5aba9ef">registerTOPPSubsection_</a>(const String &amp;name, const String &amp;description)</td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#a4455a77e7412b4bf41dbd085484196c8">require_args_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#adf95da344ba3f752eba15df253cecdde">setMaxFloat_</a>(const String &amp;name, DoubleReal max)</td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#a605edef60e83ec4fac8e06b9d8c2456b">setMaxInt_</a>(const String &amp;name, Int max)</td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#abb40d991085e7c611f6c96de6c45ddb9">setMaxNumberOfThreads</a>(int num_threads)</td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">static</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#a0c572075f31eb74105e0c6208b4aea53">setMinFloat_</a>(const String &amp;name, DoubleReal min)</td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#a50e2ac598a7f0508f871f64082b33422">setMinInt_</a>(const String &amp;name, Int min)</td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#a505102880fe265ea8560ee9136e76fc0">setValidFormats_</a>(const String &amp;name, const std::vector&lt; String &gt; &amp;formats, const bool force_OpenMS_format=true)</td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#a85b8cf00b055fed0dca275fa28c87387">setValidStrings_</a>(const String &amp;name, const std::vector&lt; String &gt; &amp;strings)</td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#ad06dbbc4e610a7896d24a024789815fd">subsections_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#a86e4ee1c76d34583514a1a0d20c465a3">subsections_TOPP_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#a6e61791b6ff20c4e71142b700b0ad79a">test_mode_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#a149061aab047b425371d4079f4a325f4">tool_description_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#a710b3279a901758436518187692fb0af">tool_name_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#a99657ef10c0478aff846bd9a2ce91ede">toolName_</a>() const </td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#a3857c6970f5c49182a97916a1aa2d555">topp_ini_file_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">protected</span><span class="mlabel">static</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#a227f68edf8608ce32984ab7b250f3d38">TOPPBase</a>(const String &amp;name, const String &amp;description, bool official=true, bool id_tag_support=false, bool require_args=true, const String &amp;version=&quot;&quot;)</td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#ab79a6a5e2a64187383b8719a803dfa26">TOPPBase</a>()</td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#a310d47c179a1698a61494439d810e501">TOPPBase</a>(const TOPPBase &amp;)</td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537ae379f86cc4ef6f5ad8eb2b414772bc0a">UNEXPECTED_RESULT</a> enum value</td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#ac74ddc700cf9fcf91d688b6d31ff9537a8216aa4b3a817cdf8c15ed32aa946e83">UNKNOWN_ERROR</a> enum value</td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#a65de5468e578e72bc9fe6f4e603a29b3">verboseVersion_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#a4e87a8f69bbc06cd56776556dc1680ed">version_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#ab1a681a54b8c67e9b99bd00e64c3c734">writeCTD_</a>()</td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#ab0d28c26fe4909b495313dcb6c9adecc">writeDebug_</a>(const String &amp;text, UInt min_level) const </td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#a1a3e3bbe05fdaad8ea45eaaac44e559e">writeDebug_</a>(const String &amp;text, const Param &amp;param, UInt min_level) const </td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#ada8464ea991bff8328219140f57f27e2">writeLog_</a>(const String &amp;text) const </td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#a36f05bcff0f3b2173f7d5762f071cfe9">writeWSDL_</a>(const String &amp;filename)</td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html#a445a6591bf0daa05be19ff3f5dea0f43">~TOPPBase</a>()</td><td class="entry"><a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
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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 11:19:27 using doxygen 1.8.5</font></TD>
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