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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_1MRMDecoy.html">MRMDecoy</a></li> </ul>
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<div class="title">MRMDecoy Member List</div> </div>
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<p>This is the complete list of members for <a class="el" href="classOpenMS_1_1MRMDecoy.html">MRMDecoy</a>, including all inherited members.</p>
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<table class="directory">
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<tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1MRMDecoy.html#a3e49895127ad86bc7be44dd58189cada">AASequenceIdentity</a>(const String &sequence, const String &decoy)</td><td class="entry"><a class="el" href="classOpenMS_1_1MRMDecoy.html">MRMDecoy</a></td><td class="entry"></td></tr>
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<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>
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<tr class="even"><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>
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<tr><td class="entry"><a class="el" href="classOpenMS_1_1MRMDecoy.html#ad52f111c105d7d46b6af3b4c9f7d48a6">correctMasses</a>(OpenMS::TargetedExperiment &exp, double mz_threshold)</td><td class="entry"><a class="el" href="classOpenMS_1_1MRMDecoy.html">MRMDecoy</a></td><td class="entry"></td></tr>
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<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>
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<tr><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>
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<tr class="even"><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>
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<tr><td class="entry"><a class="el" href="classOpenMS_1_1MRMDecoy.html#a50b43f8f144ebd9ef626b66a5f83e8cd">find_all_tryptic</a>(std::string sequence)</td><td class="entry"><a class="el" href="classOpenMS_1_1MRMDecoy.html">MRMDecoy</a></td><td class="entry"></td></tr>
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<tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1MRMDecoy.html#aec6382f8ae0830cdc5741fe83c726635">generateDecoys</a>(OpenMS::TargetedExperiment &exp, OpenMS::TargetedExperiment &dec, String method, String decoy_tag, double identity_threshold, int max_attempts, double mz_threshold, bool theoretical, double mz_shift, bool exclude_similar, double similarity_threshold, bool remove_CNterm_mods, double precursor_mass_shift)</td><td class="entry"><a class="el" href="classOpenMS_1_1MRMDecoy.html">MRMDecoy</a></td><td class="entry"></td></tr>
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<tr><td class="entry"><a class="el" href="classOpenMS_1_1MRMDecoy.html#a78ae602df1c455a57239ea4c0284a935">getDecoyIon</a>(String ionid, std::map< String, std::map< String, DoubleReal > > &decoy_ionseries)</td><td class="entry"><a class="el" href="classOpenMS_1_1MRMDecoy.html">MRMDecoy</a></td><td class="entry"></td></tr>
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<tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1MRMDecoy.html#ad03a1f97b658e2fb8c142a27b3e4ab51">getIonSeries</a>(AASequence sequence, int precursor_charge, int max_isotopes=2)</td><td class="entry"><a class="el" href="classOpenMS_1_1MRMDecoy.html">MRMDecoy</a></td><td class="entry"></td></tr>
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<tr><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>
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<tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1MRMDecoy.html#a4971483e1080b79d7a25599d90efe333">getTargetIon</a>(double ProductMZ, double mz_threshold, std::map< String, std::map< String, double > > target_ionseries)</td><td class="entry"><a class="el" href="classOpenMS_1_1MRMDecoy.html">MRMDecoy</a></td><td class="entry"></td></tr>
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<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>
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<tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1MRMDecoy.html#a2ba70deb982f7ce4a1ee5800b9e2a553">has_CNterminal_mods</a>(const OpenMS::TargetedExperiment::Peptide &peptide)</td><td class="entry"><a class="el" href="classOpenMS_1_1MRMDecoy.html">MRMDecoy</a></td><td class="entry"></td></tr>
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<tr><td class="entry"><a class="el" href="classOpenMS_1_1MRMDecoy.html#a66836b3cc8a425855e5bb96df36d6102">IonSeries</a> typedef</td><td class="entry"><a class="el" href="classOpenMS_1_1MRMDecoy.html">MRMDecoy</a></td><td class="entry"></td></tr>
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<tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1MRMDecoy.html#a2165d5a831f324e3818c94b88bfb063d">IonSeriesMapType</a> typedef</td><td class="entry"><a class="el" href="classOpenMS_1_1MRMDecoy.html">MRMDecoy</a></td><td class="entry"></td></tr>
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<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>
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<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>
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<tr><td class="entry"><a class="el" href="classOpenMS_1_1MRMDecoy.html#a68174ad2e29e0e5c551c418cc1318ade">MRMDecoy</a>()</td><td class="entry"><a class="el" href="classOpenMS_1_1MRMDecoy.html">MRMDecoy</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
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<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>
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<tr><td class="entry"><a class="el" href="classOpenMS_1_1MRMDecoy.html#a55f8941379be7a49c63aa7d4d88eee0a">PeptideTransitionMapType</a> typedef</td><td class="entry"><a class="el" href="classOpenMS_1_1MRMDecoy.html">MRMDecoy</a></td><td class="entry"></td></tr>
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<tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1MRMDecoy.html#a87ab7393ee32c7d08b5db91c4d1a95d8">PeptideVectorType</a> typedef</td><td class="entry"><a class="el" href="classOpenMS_1_1MRMDecoy.html">MRMDecoy</a></td><td class="entry"></td></tr>
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<tr><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>
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<tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1MRMDecoy.html#abb7606c8e2c53bab61362619f44b3c11">ProteinVectorType</a> typedef</td><td class="entry"><a class="el" href="classOpenMS_1_1MRMDecoy.html">MRMDecoy</a></td><td class="entry"></td></tr>
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<tr><td class="entry"><a class="el" href="classOpenMS_1_1MRMDecoy.html#a70c03bd3940e60e283e74897c82af22d">pseudoreversePeptide</a>(OpenMS::TargetedExperiment::Peptide peptide)</td><td class="entry"><a class="el" href="classOpenMS_1_1MRMDecoy.html">MRMDecoy</a></td><td class="entry"></td></tr>
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<tr class="even"><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>
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<tr><td class="entry"><a class="el" href="classOpenMS_1_1MRMDecoy.html#a6a06fa868219541393df9ca8c23324bb">restrictTransitions</a>(OpenMS::TargetedExperiment &exp, int min_transitions, int max_transitions)</td><td class="entry"><a class="el" href="classOpenMS_1_1MRMDecoy.html">MRMDecoy</a></td><td class="entry"></td></tr>
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<tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1MRMDecoy.html#a9986d344ee00c124870884f6a476b90d">reversePeptide</a>(OpenMS::TargetedExperiment::Peptide peptide)</td><td class="entry"><a class="el" href="classOpenMS_1_1MRMDecoy.html">MRMDecoy</a></td><td class="entry"></td></tr>
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<tr><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>
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<tr class="even"><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>
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<tr><td class="entry"><a class="el" href="classOpenMS_1_1MRMDecoy.html#ad121f448031c8a2d2ea44cf760d9220b">shufflePeptide</a>(OpenMS::TargetedExperiment::Peptide peptide, double identity_threshold, int seed=-1, int max_attempts=10)</td><td class="entry"><a class="el" href="classOpenMS_1_1MRMDecoy.html">MRMDecoy</a></td><td class="entry"></td></tr>
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<tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1ProgressLogger.html#af1c45ecd71b5041b70319249e8e73591">startProgress</a>(SignedSize begin, SignedSize end, const String &label) const </td><td class="entry"><a class="el" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a></td><td class="entry"></td></tr>
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<tr><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>
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<tr class="even"><td class="entry"><a class="el" href="classOpenMS_1_1MRMDecoy.html#a7a9324ee2f11d04b8cab4e4d9c6d750e">TransitionVectorType</a> typedef</td><td class="entry"><a class="el" href="classOpenMS_1_1MRMDecoy.html">MRMDecoy</a></td><td class="entry"></td></tr>
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<tr><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>
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<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>
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<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>
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<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:27 using doxygen 1.8.5</font></TD>
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