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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_1PSLPFormulation.html">PSLPFormulation</a></li>  </ul>
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<p>This is the complete list of members for <a class="el" href="classOpenMS_1_1PSLPFormulation.html">PSLPFormulation</a>, including all inherited members.</p>
<table class="directory">
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1PSLPFormulation.html#acb8e7e2fdca6e28e41ccf00804745831">addMaxInclusionListSizeConstraints_</a>(std::vector&lt; IndexTriple &gt; &amp;variable_indices, UInt max_list_size)</td><td class="entry"><a class="el" href="classOpenMS_1_1PSLPFormulation.html">PSLPFormulation</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1PSLPFormulation.html#ae9b0d6ee22f04f0a1ddabd628521bb08">addPrecursorAcquisitionNumberConstraint_</a>(std::vector&lt; IndexTriple &gt; &amp;variable_indices, Size number_of_features, UInt number_of_msms_per_precursor)</td><td class="entry"><a class="el" href="classOpenMS_1_1PSLPFormulation.html">PSLPFormulation</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1PSLPFormulation.html#a7f90dbe3e72b9b6245c32206d9c2df47">addProteinCoverageConstraint_</a>(std::vector&lt; IndexTriple &gt; &amp;variable_indices, PrecursorIonSelectionPreprocessing &amp;preprocessing, std::map&lt; String, Size &gt; protein_variable_index_map)</td><td class="entry"><a class="el" href="classOpenMS_1_1PSLPFormulation.html">PSLPFormulation</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1PSLPFormulation.html#aacbd6aaa0fadc5a38bd714b16a01df01">addProteinToILP_</a>(PrecursorIonSelectionPreprocessing &amp;preprocessing, std::map&lt; String, std::vector&lt; DoubleReal &gt; &gt;::const_iterator map_iter, Size &amp;counter, Size &amp;pep_counter, Size &amp;feature_counter, std::vector&lt; IndexTriple &gt; &amp;variable_indices, std::map&lt; String, Size &gt; &amp;protein_penalty_index_map, FeatureMap&lt;&gt; &amp;precursors)</td><td class="entry"><a class="el" href="classOpenMS_1_1PSLPFormulation.html">PSLPFormulation</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1PSLPFormulation.html#a3c1ef316108b552bb3e1d52eb5cf3be7">addRTBinCapacityConstraint_</a>(std::vector&lt; IndexTriple &gt; &amp;variable_indices, Size max_rt_index, UInt ms2_spectra_per_rt_bin, bool sequential_order=false)</td><td class="entry"><a class="el" href="classOpenMS_1_1PSLPFormulation.html">PSLPFormulation</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1PSLPFormulation.html#ab8929efe83b307a688a4bd616e5b6394">addStepSizeConstraint_</a>(std::vector&lt; IndexTriple &gt; &amp;variable_indices, UInt step_size)</td><td class="entry"><a class="el" href="classOpenMS_1_1PSLPFormulation.html">PSLPFormulation</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1PSLPFormulation.html#ae86c2a4f209949045780102c2476cede">assembleInclusionListForProteinBasedLP_</a>(std::vector&lt; IndexTriple &gt; &amp;variable_indices, FeatureMap&lt;&gt; &amp;precursors, std::vector&lt; int &gt; &amp;solution_indices, PrecursorIonSelectionPreprocessing &amp;preprocessing)</td><td class="entry"><a class="el" href="classOpenMS_1_1PSLPFormulation.html">PSLPFormulation</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1PSLPFormulation.html#a8a38d766081c104c51a498b4d836a456">calculateXICs_</a>(std::vector&lt; std::vector&lt; DoubleReal &gt; &gt; &amp;xics, const FeatureMap&lt;&gt; &amp;features, const MSExperiment&lt; InputPeakType &gt; &amp;experiment, const std::vector&lt; std::vector&lt; std::pair&lt; Size, Size &gt; &gt; &gt; &amp;mass_ranges, const bool normalize)</td><td class="entry"><a class="el" href="classOpenMS_1_1PSLPFormulation.html">PSLPFormulation</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#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_1PSLPFormulation.html#a1086e2f906cf141a7bd2b42da33126b2">createAndSolveCombinedLPFeatureBased_</a>(const FeatureMap&lt;&gt; &amp;features, std::vector&lt; std::vector&lt; DoubleReal &gt; &gt; &amp;intensity_weights, std::set&lt; Int &gt; &amp;charges_set, std::vector&lt; std::vector&lt; std::pair&lt; Size, Size &gt; &gt; &gt; &amp;mass_ranges, std::vector&lt; IndexTriple &gt; &amp;variable_indices, std::vector&lt; Int &gt; &amp;solution_indices, UInt ms2_spectra_per_rt_bin, Size number_of_scans, Size step_size=0, bool sequential_order=false)</td><td class="entry"><a class="el" href="classOpenMS_1_1PSLPFormulation.html">PSLPFormulation</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1PSLPFormulation.html#a79f7295c0f12730a06e4e2c871f6a322">createAndSolveCombinedLPForKnownLCMSMapFeatureBased</a>(const FeatureMap&lt;&gt; &amp;features, const MSExperiment&lt; InputPeakType &gt; &amp;experiment, std::vector&lt; IndexTriple &gt; &amp;variable_indices, std::vector&lt; int &gt; &amp;solution_indices, std::vector&lt; std::vector&lt; std::pair&lt; Size, Size &gt; &gt; &gt; &amp;mass_ranges, std::set&lt; Int &gt; &amp;charges_set, UInt ms2_spectra_per_rt_bin, Size step_size=0, bool sequential_order=false)</td><td class="entry"><a class="el" href="classOpenMS_1_1PSLPFormulation.html">PSLPFormulation</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1PSLPFormulation.html#abf5924afa9c5296213f21da56c7727c5">createAndSolveILP_</a>(const FeatureMap&lt;&gt; &amp;features, std::vector&lt; std::vector&lt; DoubleReal &gt; &gt; &amp;intensity_weights, std::set&lt; Int &gt; &amp;charges_set, std::vector&lt; std::vector&lt; std::pair&lt; Size, Size &gt; &gt; &gt; &amp;mass_ranges, std::vector&lt; IndexTriple &gt; &amp;variable_indices, std::vector&lt; int &gt; &amp;solution_indices, UInt ms2_spectra_per_rt_bin, Size number_of_scans)</td><td class="entry"><a class="el" href="classOpenMS_1_1PSLPFormulation.html">PSLPFormulation</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1PSLPFormulation.html#a7016966748e94bd9bc195d074421a6a7">createAndSolveILPForInclusionListCreation</a>(PrecursorIonSelectionPreprocessing &amp;preprocessing, UInt ms2_spectra_per_rt_bin, UInt max_list_size, FeatureMap&lt;&gt; &amp;precursors, bool solve_ILP=true)</td><td class="entry"><a class="el" href="classOpenMS_1_1PSLPFormulation.html">PSLPFormulation</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1PSLPFormulation.html#a2a93e2928cdbb7704c7d49a33f13b091">createAndSolveILPForKnownLCMSMapFeatureBased</a>(const FeatureMap&lt;&gt; &amp;features, const MSExperiment&lt; InputPeakType &gt; &amp;experiment, std::vector&lt; IndexTriple &gt; &amp;variable_indices, std::vector&lt; std::vector&lt; std::pair&lt; Size, Size &gt; &gt; &gt; &amp;mass_ranges, std::set&lt; Int &gt; &amp;charges_set, UInt ms2_spectra_per_rt_bin, std::vector&lt; int &gt; &amp;solution_indices)</td><td class="entry"><a class="el" href="classOpenMS_1_1PSLPFormulation.html">PSLPFormulation</a></td><td class="entry"></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_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><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_1PSLPFormulation.html#ac945a0966726a3a644d194b81c28d960">getLPSolver</a>()</td><td class="entry"><a class="el" href="classOpenMS_1_1PSLPFormulation.html">PSLPFormulation</a></td><td class="entry"><span class="mlabel">inline</span></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_1PSLPFormulation.html#a9d8beee78137a31458805ed79ae90738">getNumberOfPrecsInSpectrum_</a>(Int constr_idx)</td><td class="entry"><a class="el" href="classOpenMS_1_1PSLPFormulation.html">PSLPFormulation</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><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 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_1PSLPFormulation.html#a350a55d7f8d02185064c3682c0a4d7f8">getXIC_</a>(const std::vector&lt; std::pair&lt; Size, Size &gt; &gt; &amp;end_points, std::vector&lt; DoubleReal &gt; &amp;weights, const MSExperiment&lt; InputPeakType &gt; &amp;experiment, const bool normalize)</td><td class="entry"><a class="el" href="classOpenMS_1_1PSLPFormulation.html">PSLPFormulation</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1PSLPFormulation.html#a3fde56a178e0bdc00cd84a011415ee41">model_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1PSLPFormulation.html">PSLPFormulation</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#ae6b6d68036a573a44f6609460ba2dfb6">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 class="even"><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><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 class="even"><td class="entry"><a class="el" href="classOpenMS_1_1PSLPFormulation.html#a5978209f8f414bcd126c98e0a3ec0732">PSLPFormulation</a>()</td><td class="entry"><a class="el" href="classOpenMS_1_1PSLPFormulation.html">PSLPFormulation</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1PSLPFormulation.html#a2b206fdbe8649b90b854129f37fc594a">setLPSolver</a>(LPWrapper::SOLVER solver)</td><td class="entry"><a class="el" href="classOpenMS_1_1PSLPFormulation.html">PSLPFormulation</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
  <tr class="even"><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><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 class="even"><td class="entry"><a class="el" href="classOpenMS_1_1PSLPFormulation.html#ab5958e31e458230f7587571d8e88df72">solveILP</a>(std::vector&lt; int &gt; &amp;solution_indices)</td><td class="entry"><a class="el" href="classOpenMS_1_1PSLPFormulation.html">PSLPFormulation</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1PSLPFormulation.html#afb8f1202d548f01394d85fbeb51f9adf">solver_</a></td><td class="entry"><a class="el" href="classOpenMS_1_1PSLPFormulation.html">PSLPFormulation</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#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><td class="entry"><a class="el" href="classOpenMS_1_1PSLPFormulation.html#ae13f18cf17e4d034b47b08370645c9cd">updateCombinedILP</a>(FeatureMap&lt;&gt; &amp;features, PrecursorIonSelectionPreprocessing &amp;preprocessed_db, std::vector&lt; IndexTriple &gt; &amp;variable_indices, std::vector&lt; String &gt; &amp;new_protein_accs, std::vector&lt; String &gt; &amp;protein_accs, PSProteinInference &amp;prot_inference, Size &amp;variable_counter, std::map&lt; String, std::vector&lt; Size &gt; &gt; &amp;protein_feature_map, Feature &amp;new_feature, std::map&lt; String, Size &gt; &amp;protein_variable_index_map, std::map&lt; String, std::set&lt; String &gt; &gt; &amp;prot_id_counter)</td><td class="entry"><a class="el" href="classOpenMS_1_1PSLPFormulation.html">PSLPFormulation</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1PSLPFormulation.html#af04d2257211680eeee22ecfc3908f95c">updateFeatureILPVariables</a>(FeatureMap&lt;&gt; &amp;new_features, std::vector&lt; IndexTriple &gt; &amp;variable_indices, std::map&lt; Size, std::vector&lt; String &gt; &gt; &amp;feature_constraints_map)</td><td class="entry"><a class="el" href="classOpenMS_1_1PSLPFormulation.html">PSLPFormulation</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a776f7572fc4f466e9527ca233471920d">updateMembers_</a>()</td><td class="entry"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td><td class="entry"><span class="mlabel">protected</span><span class="mlabel">virtual</span></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1PSLPFormulation.html#a5dd6992bb90f2e509ceee96ef3653579">updateObjFunction_</a>(String acc, FeatureMap&lt;&gt; &amp;features, PrecursorIonSelectionPreprocessing &amp;preprocessed_db, std::vector&lt; IndexTriple &gt; &amp;variable_indices)</td><td class="entry"><a class="el" href="classOpenMS_1_1PSLPFormulation.html">PSLPFormulation</a></td><td class="entry"><span class="mlabel">protected</span></td></tr>
  <tr><td class="entry"><a class="el" href="classOpenMS_1_1PSLPFormulation.html#aae5b548ad11c08ee6a117ac4109e38ee">updateRTConstraintsForSequentialILP</a>(Size &amp;rt_index, UInt ms2_spectra_per_rt_bin, Size max_rt_index)</td><td class="entry"><a class="el" href="classOpenMS_1_1PSLPFormulation.html">PSLPFormulation</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1PSLPFormulation.html#a0cfcde3e24f3bee199dd5b9642cf26f7">updateStepSizeConstraint</a>(Size iteration, UInt step_size)</td><td class="entry"><a class="el" href="classOpenMS_1_1PSLPFormulation.html">PSLPFormulation</a></td><td class="entry"></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_1PSLPFormulation.html#a10f8bea2cb7be3cc254e690a379275df">~PSLPFormulation</a>()</td><td class="entry"><a class="el" href="classOpenMS_1_1PSLPFormulation.html">PSLPFormulation</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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