File: classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment-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_1MapAlignmentAlgorithmSpectrumAlignment.html">MapAlignmentAlgorithmSpectrumAlignment</a></li>  </ul>
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<p>This is the complete list of members for <a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html">MapAlignmentAlgorithmSpectrumAlignment</a>, including all inherited members.</p>
<table class="directory">
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a7141ee1dd0cfb6b893aa77cb2a29bd9e">affineGapalign_</a>(Size xbegin, Size ybegin, Size xend, Size yend, const std::vector&lt; MSSpectrum&lt;&gt; * &gt; &amp;pattern, std::vector&lt; MSSpectrum&lt;&gt; * &gt; &amp;aligned, std::vector&lt; int &gt; &amp;xcoordinate, std::vector&lt; Real &gt; &amp;ycoordinate, std::vector&lt; int &gt; &amp;xcoordinatepattern)</td><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html">MapAlignmentAlgorithmSpectrumAlignment</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithm.html#a9e66a73174d03975d49a7e9b3f8854df">alignCompactFeatureMaps</a>(std::vector&lt; std::vector&lt; Peak2D &gt; &gt; &amp;, std::vector&lt; TransformationDescription &gt; &amp;)</td><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithm.html">MapAlignmentAlgorithm</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithm.html#a7385e8b646ae9d282c3c06abf1620083">alignConsensusMaps</a>(std::vector&lt; ConsensusMap &gt; &amp;, std::vector&lt; TransformationDescription &gt; &amp;)</td><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithm.html">MapAlignmentAlgorithm</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithm.html#a32c9e0577b4455dbc2d3493079ef1c81">alignFeatureMaps</a>(std::vector&lt; FeatureMap&lt;&gt; &gt; &amp;, std::vector&lt; TransformationDescription &gt; &amp;)</td><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithm.html">MapAlignmentAlgorithm</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a2038727c06b2e23bf60e1d21d7179815">alignPeakMaps</a>(std::vector&lt; MSExperiment&lt;&gt; &gt; &amp;, std::vector&lt; TransformationDescription &gt; &amp;)</td><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html">MapAlignmentAlgorithmSpectrumAlignment</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithm.html#a4f223602464cbafef563871036b5dfc1">alignPeptideIdentifications</a>(std::vector&lt; std::vector&lt; PeptideIdentification &gt; &gt; &amp;, std::vector&lt; TransformationDescription &gt; &amp;)</td><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithm.html">MapAlignmentAlgorithm</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a4e8ad8a7db1b7e3ee65134b631931a1a">anchorPoints_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html">MapAlignmentAlgorithmSpectrumAlignment</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a56589612e0e4164bf80c3918a087d05a">begin_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a></td><td class="entry"><span class="mlabel">mutable</span><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a3b40e068d05ddb744123900a90148d94">bestk_</a>(const std::vector&lt; MSSpectrum&lt;&gt; * &gt; &amp;pattern, std::vector&lt; MSSpectrum&lt;&gt; * &gt; &amp;aligned, std::map&lt; Size, std::map&lt; Size, Real &gt; &gt; &amp;buffer, bool column_row_orientation, Size xbegin, Size xend, Size ybegin, Size yend)</td><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html">MapAlignmentAlgorithmSpectrumAlignment</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a1a04c61f71e0325273f9e89cdc1c5a67">bucketFilter_</a>(const std::vector&lt; MSSpectrum&lt;&gt; * &gt; &amp;pattern, std::vector&lt; MSSpectrum&lt;&gt; * &gt; &amp;aligned, std::vector&lt; Int &gt; &amp;xcoordinate, std::vector&lt; Real &gt; &amp;ycoordinate, std::vector&lt; Int &gt; &amp;xcoordinatepattern)</td><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html">MapAlignmentAlgorithmSpectrumAlignment</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a23c2cf21022e3e7bf4e9b82919dba1b8">bucketsize_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html">MapAlignmentAlgorithmSpectrumAlignment</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#ab890c00034eaf606dcd4438319dac090">c1_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html">MapAlignmentAlgorithmSpectrumAlignment</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a7c3b265b697a57615da5cd3274780efd">check_defaults_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87ca3ab34dd50405af2d5a62627d572f7860">CMD</a> enum value</td><td class="entry"><a class="el" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a9584ec9238430832ac2c381039513247">create</a>()</td><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html">MapAlignmentAlgorithmSpectrumAlignment</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">static</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#ab194d52a2d0143fcdb17c626ebaaf588">cutoffScore_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html">MapAlignmentAlgorithmSpectrumAlignment</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#afa3f4fa08a8a3b675e2dab06e29412a1">debug_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html">MapAlignmentAlgorithmSpectrumAlignment</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#af6a7c231cbbebdb557a892af1c22b146">debugFileCreator_</a>(const std::vector&lt; MSSpectrum&lt;&gt; * &gt; &amp;pattern, std::vector&lt; MSSpectrum&lt;&gt; * &gt; &amp;aligned)</td><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html">MapAlignmentAlgorithmSpectrumAlignment</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a0a9eefab469443f2ac99f95d3ffa167f">debugmatrix_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html">MapAlignmentAlgorithmSpectrumAlignment</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a1809434361710cb8459386366900d35a">debugscoreDistributionCalculation_</a>(Real score)</td><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html">MapAlignmentAlgorithmSpectrumAlignment</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a3d66c4ad95892c40bce2188850fb36d8">debugscorematrix_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html">MapAlignmentAlgorithmSpectrumAlignment</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#ac7c42fdddecd7a8212baa9bfa43ff958">debugtraceback_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html">MapAlignmentAlgorithmSpectrumAlignment</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#afb6802fda161cb0c1a4a05597f94aecc">DefaultParamHandler</a>(const String &amp;name)</td><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a954da7eef3cfddda446574eaadd20abb">DefaultParamHandler</a>(const DefaultParamHandler &amp;rhs)</td><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a2802c591e6d7fd3fd9cc35f5e875d0ba">defaultsToParam_</a>()</td><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a76072b3919abcf01141ba68da8a001fd">dlg_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a></td><td class="entry"><span class="mlabel">mutable</span><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a5f4343fd568e4980066be6af2eef3351">e_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html">MapAlignmentAlgorithmSpectrumAlignment</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a0c749bf4e621699b7a5c45ae22c2fa90">end_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a></td><td class="entry"><span class="mlabel">mutable</span><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a1cc1012b0cdaea97f58d571af1ff45de">endProgress</a>() const </td><td class="entry"><a class="el" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#ad39786131abad2728aeada5bd882c264">eraseFloatDataArrayEntry_</a>(std::vector&lt; MSSpectrum&lt;&gt; * &gt; &amp;spectrum_pointer_container)</td><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html">MapAlignmentAlgorithmSpectrumAlignment</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a5a51f3f150b09068256195e934339a19">error_name_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithm.html#acc270843ebe2525547c6ac01bf341234">fitModel</a>(const String &amp;model_type, const Param &amp;params, std::vector&lt; TransformationDescription &gt; &amp;trafos)</td><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithm.html">MapAlignmentAlgorithm</a></td><td class="entry"><span class="mlabel">static</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#ad60d86ce26e0eb12d4c4917de4cae236">fourierActivation_</a>(std::vector&lt; MSSpectrum&lt;&gt; * &gt; &amp;spectrum_pointer_container)</td><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html">MapAlignmentAlgorithmSpectrumAlignment</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a0bfda7af52aef129dd99f8664efd3da8">gap_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html">MapAlignmentAlgorithmSpectrumAlignment</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a02f02fa9832ca3e8d47c575a39803a2a">getDefaults</a>() const </td><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a67024cdd5c34ec571baecabd8f783310">getLogType</a>() const </td><td class="entry"><a class="el" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#aaee0f2845288173de9f6ad47e6ad31d5">getName</a>() const </td><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a7f6aab5a7dfbdd1c062a4352a29361f3">getParameters</a>() const </td><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a8d4600093afb26cff7d7db82a1837e9f">getProductName</a>()</td><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html">MapAlignmentAlgorithmSpectrumAlignment</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">static</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a768d4a2093627a2f34728656a9721bdf">getSubsections</a>() const </td><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87ca73c6901c7c648a6a735770bc038bb26a">GUI</a> enum value</td><td class="entry"><a class="el" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a9722326c38c717ec2e0eea7955aed051">insideBand_</a>(Size i, Size j, Size n, Size m, Int k_)</td><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html">MapAlignmentAlgorithmSpectrumAlignment</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a79bacf60c4109d7517590441c7f85f9c">last_invoke_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a></td><td class="entry"><span class="mlabel">mutable</span><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87c">LogType</a> enum name</td><td class="entry"><a class="el" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithm.html#a2323adcbf2f7ef45c0a4c63f0001374a">MapAlignmentAlgorithm</a>()</td><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithm.html">MapAlignmentAlgorithm</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a0871a5000159ab5a2f3b79d92760665f">MapAlignmentAlgorithmSpectrumAlignment</a>()</td><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html">MapAlignmentAlgorithmSpectrumAlignment</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a6bc1d6b26465ed9cbf771c2cb0ad4313">MapAlignmentAlgorithmSpectrumAlignment</a>(const MapAlignmentAlgorithmSpectrumAlignment &amp;)</td><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html">MapAlignmentAlgorithmSpectrumAlignment</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#af300c42aaa79482d8acadf3470835ab8">mismatchscore_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html">MapAlignmentAlgorithmSpectrumAlignment</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#ada98b6ec65437d5660a8bf43e1bc15fc">msFilter_</a>(MSExperiment&lt;&gt; &amp;peakmap, std::vector&lt; MSSpectrum&lt;&gt; * &gt; &amp;spectrum_pointer_container)</td><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html">MapAlignmentAlgorithmSpectrumAlignment</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87cac157bdf0b85a40d2619cbc8bc1ae5fe2">NONE</a> enum value</td><td class="entry"><a class="el" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#ac24b9ad324036fbcb50828e3b9268d1e">operator=</a>(const MapAlignmentAlgorithmSpectrumAlignment &amp;)</td><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html">MapAlignmentAlgorithmSpectrumAlignment</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#ae6b6d68036a573a44f6609460ba2dfb6">OpenMS::DefaultParamHandler::operator=</a>(const DefaultParamHandler &amp;rhs)</td><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#ac435f2dd4d9f9328db83af97129a8d7e">operator==</a>(const DefaultParamHandler &amp;rhs) const </td><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a028b9561e7458f15cc08cba7238118b7">prepareAlign_</a>(const std::vector&lt; MSSpectrum&lt;&gt; * &gt; &amp;pattern, MSExperiment&lt;&gt; &amp;aligned, std::vector&lt; TransformationDescription &gt; &amp;transformation)</td><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html">MapAlignmentAlgorithmSpectrumAlignment</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a2a106011aec95b2013d7a545f2063d01">ProgressLogger</a>()</td><td class="entry"><a class="el" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a94eb3ef5ef94b83eb348dd00a2b53119">recursion_depth_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a></td><td class="entry"><span class="mlabel">protected</span><span class="mlabel">static</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithm.html#a7899dbe105534dc1f81971dd71a26ff0">registerChildren</a>()</td><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithm.html">MapAlignmentAlgorithm</a></td><td class="entry"><span class="mlabel">static</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a7be42d61be33e31f1725bc3a4e84935c">scoreCalculation_</a>(Size i, Size j, Size patternbegin, Size alignbegin, const std::vector&lt; MSSpectrum&lt;&gt; * &gt; &amp;pattern, std::vector&lt; MSSpectrum&lt;&gt; * &gt; &amp;aligned, std::map&lt; Size, std::map&lt; Size, Real &gt; &gt; &amp;buffer, bool column_row_orientation)</td><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html">MapAlignmentAlgorithmSpectrumAlignment</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a8e7a8926f87a4a4709278d537577e4f8">scoredistribution_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html">MapAlignmentAlgorithmSpectrumAlignment</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a33e063cd96aaa8be717605e697029a54">scoring_</a>(const MSSpectrum&lt;&gt; &amp;a, MSSpectrum&lt;&gt; &amp;b)</td><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html">MapAlignmentAlgorithmSpectrumAlignment</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1ProgressLogger.html#acc3538c5284777d8702ccaefeb61e74c">setLogType</a>(LogType type) const </td><td class="entry"><a class="el" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a77d37f2e1c12e8bd33ea0e660a89e927">setName</a>(const String &amp;name)</td><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#abc8067511cfc949ae942ea2b08588f81">setParameters</a>(const Param &amp;param)</td><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a8852277abd03220cc7b80d6c1bed6fed">setProgress</a>(SignedSize value) const </td><td class="entry"><a class="el" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithm.html#aef01d65c73bbdd9f550309195007622b">setReference</a>(Size reference_index=0, const String &amp;reference_file=&quot;&quot;)</td><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithm.html">MapAlignmentAlgorithm</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1ProgressLogger.html#af1c45ecd71b5041b70319249e8e73591">startProgress</a>(SignedSize begin, SignedSize end, const String &amp;label) const </td><td class="entry"><a class="el" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a6d9750520313ea7f843d7a49cb2e9e5f">stop_watch_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a></td><td class="entry"><span class="mlabel">mutable</span><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#ac4b0e20bc59c7a5afe016c69067e428c">subsections_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a9b1cc0d5756927db86ca7ef37148b812">threshold_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html">MapAlignmentAlgorithmSpectrumAlignment</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a2bc102affe34d954f253f24a0f1673f4">transform_</a>(MSSpectrum&lt;&gt; &amp;spec)</td><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html">MapAlignmentAlgorithmSpectrumAlignment</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a7c691d7de2a43bc5606e96cb15da3641">type_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a></td><td class="entry"><span class="mlabel">mutable</span><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#aaf258e1a9846d9b238ee4b3005ad3ee9">updateMembers_</a>()</td><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html">MapAlignmentAlgorithmSpectrumAlignment</a></td><td class="entry"><span class="mlabel">private</span><span class="mlabel">virtual</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1ProgressLogger.html#aec57b26e143202dc119a41592e075932">value_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a></td><td class="entry"><span class="mlabel">mutable</span><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#aba444910e4fccb93f91bf7ab135f508a">warn_empty_defaults_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a11e9d6dd34fe8860874aa8abe0ec121b">~DefaultParamHandler</a>()</td><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithm.html#a1423ba5efed91566183b0d264fe0c2fe">~MapAlignmentAlgorithm</a>()</td><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithm.html">MapAlignmentAlgorithm</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a4b7f0f53c53352adb66f334fb5dd0a2b">~MapAlignmentAlgorithmSpectrumAlignment</a>()</td><td class="entry"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html">MapAlignmentAlgorithmSpectrumAlignment</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a19c882d907f90f7f88c7436d82cd2a13">~ProgressLogger</a>()</td><td class="entry"><a class="el" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a></td><td class="entry"></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 11:19:26 using doxygen 1.8.5</font></TD>
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