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<li class="navelem"><a class="el" href="dir_e770f0cf77e550adde3f44739ef529fe.html">include</a></li><li class="navelem"><a class="el" href="dir_6a63c4937d4da007e55fff5dcf71e0f8.html">OpenMS</a></li><li class="navelem"><a class="el" href="dir_330fe73d44ce641f33dd6036f80161a5.html">ANALYSIS</a></li><li class="navelem"><a class="el" href="dir_432be27a4896f4299230a7289acf24ab.html">TARGETED</a></li>  </ul>
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<div class="title">TargetedExperiment.h</div>  </div>
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<a href="TargetedExperiment_8h.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno">    1</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00002"></a><span class="lineno">    2</span>&#160;<span class="comment">//                   OpenMS -- Open-Source Mass Spectrometry</span></div>
<div class="line"><a name="l00003"></a><span class="lineno">    3</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00004"></a><span class="lineno">    4</span>&#160;<span class="comment">// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,</span></div>
<div class="line"><a name="l00005"></a><span class="lineno">    5</span>&#160;<span class="comment">// ETH Zurich, and Freie Universitaet Berlin 2002-2013.</span></div>
<div class="line"><a name="l00006"></a><span class="lineno">    6</span>&#160;<span class="comment">//</span></div>
<div class="line"><a name="l00007"></a><span class="lineno">    7</span>&#160;<span class="comment">// This software is released under a three-clause BSD license:</span></div>
<div class="line"><a name="l00008"></a><span class="lineno">    8</span>&#160;<span class="comment">//  * Redistributions of source code must retain the above copyright</span></div>
<div class="line"><a name="l00009"></a><span class="lineno">    9</span>&#160;<span class="comment">//    notice, this list of conditions and the following disclaimer.</span></div>
<div class="line"><a name="l00010"></a><span class="lineno">   10</span>&#160;<span class="comment">//  * Redistributions in binary form must reproduce the above copyright</span></div>
<div class="line"><a name="l00011"></a><span class="lineno">   11</span>&#160;<span class="comment">//    notice, this list of conditions and the following disclaimer in the</span></div>
<div class="line"><a name="l00012"></a><span class="lineno">   12</span>&#160;<span class="comment">//    documentation and/or other materials provided with the distribution.</span></div>
<div class="line"><a name="l00013"></a><span class="lineno">   13</span>&#160;<span class="comment">//  * Neither the name of any author or any participating institution</span></div>
<div class="line"><a name="l00014"></a><span class="lineno">   14</span>&#160;<span class="comment">//    may be used to endorse or promote products derived from this software</span></div>
<div class="line"><a name="l00015"></a><span class="lineno">   15</span>&#160;<span class="comment">//    without specific prior written permission.</span></div>
<div class="line"><a name="l00016"></a><span class="lineno">   16</span>&#160;<span class="comment">// For a full list of authors, refer to the file AUTHORS.</span></div>
<div class="line"><a name="l00017"></a><span class="lineno">   17</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00018"></a><span class="lineno">   18</span>&#160;<span class="comment">// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS &quot;AS IS&quot;</span></div>
<div class="line"><a name="l00019"></a><span class="lineno">   19</span>&#160;<span class="comment">// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE</span></div>
<div class="line"><a name="l00020"></a><span class="lineno">   20</span>&#160;<span class="comment">// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE</span></div>
<div class="line"><a name="l00021"></a><span class="lineno">   21</span>&#160;<span class="comment">// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING</span></div>
<div class="line"><a name="l00022"></a><span class="lineno">   22</span>&#160;<span class="comment">// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,</span></div>
<div class="line"><a name="l00023"></a><span class="lineno">   23</span>&#160;<span class="comment">// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,</span></div>
<div class="line"><a name="l00024"></a><span class="lineno">   24</span>&#160;<span class="comment">// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;</span></div>
<div class="line"><a name="l00025"></a><span class="lineno">   25</span>&#160;<span class="comment">// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,</span></div>
<div class="line"><a name="l00026"></a><span class="lineno">   26</span>&#160;<span class="comment">// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR</span></div>
<div class="line"><a name="l00027"></a><span class="lineno">   27</span>&#160;<span class="comment">// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF</span></div>
<div class="line"><a name="l00028"></a><span class="lineno">   28</span>&#160;<span class="comment">// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</span></div>
<div class="line"><a name="l00029"></a><span class="lineno">   29</span>&#160;<span class="comment">//</span></div>
<div class="line"><a name="l00030"></a><span class="lineno">   30</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00031"></a><span class="lineno">   31</span>&#160;<span class="comment">// $Maintainer: Hannes Roest $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160;<span class="comment">// $Authors: Andreas Bertsch $</span></div>
<div class="line"><a name="l00033"></a><span class="lineno">   33</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00034"></a><span class="lineno">   34</span>&#160;</div>
<div class="line"><a name="l00035"></a><span class="lineno">   35</span>&#160;<span class="preprocessor">#ifndef OPENMS_ANALYSIS_TARGETED_TARGETEDEXPERIMENT_H</span></div>
<div class="line"><a name="l00036"></a><span class="lineno">   36</span>&#160;<span class="preprocessor"></span><span class="preprocessor">#define OPENMS_ANALYSIS_TARGETED_TARGETEDEXPERIMENT_H</span></div>
<div class="line"><a name="l00037"></a><span class="lineno">   37</span>&#160;<span class="preprocessor"></span></div>
<div class="line"><a name="l00038"></a><span class="lineno">   38</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="StandardTypes_8h.html">OpenMS/KERNEL/StandardTypes.h</a>&gt;</span></div>
<div class="line"><a name="l00039"></a><span class="lineno">   39</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="ReactionMonitoringTransition_8h.html">OpenMS/ANALYSIS/MRM/ReactionMonitoringTransition.h</a>&gt;</span></div>
<div class="line"><a name="l00040"></a><span class="lineno">   40</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="IncludeExcludeTarget_8h.html">OpenMS/ANALYSIS/TARGETED/IncludeExcludeTarget.h</a>&gt;</span></div>
<div class="line"><a name="l00041"></a><span class="lineno">   41</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="CVTerm_8h.html">OpenMS/METADATA/CVTerm.h</a>&gt;</span></div>
<div class="line"><a name="l00042"></a><span class="lineno">   42</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="CVTermList_8h.html">OpenMS/METADATA/CVTermList.h</a>&gt;</span></div>
<div class="line"><a name="l00043"></a><span class="lineno">   43</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="Software_8h.html">OpenMS/METADATA/Software.h</a>&gt;</span></div>
<div class="line"><a name="l00044"></a><span class="lineno">   44</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="TargetedExperimentHelper_8h.html">OpenMS/ANALYSIS/TARGETED/TargetedExperimentHelper.h</a>&gt;</span></div>
<div class="line"><a name="l00045"></a><span class="lineno">   45</span>&#160;</div>
<div class="line"><a name="l00046"></a><span class="lineno">   46</span>&#160;<span class="preprocessor">#include &lt;vector&gt;</span></div>
<div class="line"><a name="l00047"></a><span class="lineno">   47</span>&#160;</div>
<div class="line"><a name="l00048"></a><span class="lineno">   48</span>&#160;<span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00049"></a><span class="lineno">   49</span>&#160;{</div>
<div class="line"><a name="l00053"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TargetedExperiment.html">   53</a></span>&#160;  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1TargetedExperiment.html">TargetedExperiment</a></div>
<div class="line"><a name="l00054"></a><span class="lineno">   54</span>&#160;  {</div>
<div class="line"><a name="l00055"></a><span class="lineno">   55</span>&#160;<span class="keyword">public</span>:</div>
<div class="line"><a name="l00056"></a><span class="lineno">   56</span>&#160;</div>
<div class="line"><a name="l00057"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TargetedExperiment.html#abd581285516dfa4bdd8753a5568931d3">   57</a></span>&#160;    <span class="keyword">typedef</span> <a class="code" href="structOpenMS_1_1TargetedExperimentHelper_1_1CV.html">TargetedExperimentHelper::CV</a> <a class="code" href="classOpenMS_1_1TargetedExperiment.html#abd581285516dfa4bdd8753a5568931d3">CV</a>;</div>
<div class="line"><a name="l00058"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TargetedExperiment.html#a6be5011e53737493e15d175f5d4a1d03">   58</a></span>&#160;    <span class="keyword">typedef</span> <a class="code" href="structOpenMS_1_1TargetedExperimentHelper_1_1Protein.html">TargetedExperimentHelper::Protein</a> <a class="code" href="classOpenMS_1_1TargetedExperiment.html#a6be5011e53737493e15d175f5d4a1d03">Protein</a>;</div>
<div class="line"><a name="l00059"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TargetedExperiment.html#aecbf6dcfb8bc066ff62e1ef0a7d655bf">   59</a></span>&#160;    <span class="keyword">typedef</span> <a class="code" href="classOpenMS_1_1TargetedExperimentHelper_1_1RetentionTime.html">TargetedExperimentHelper::RetentionTime</a> <a class="code" href="classOpenMS_1_1TargetedExperiment.html#aecbf6dcfb8bc066ff62e1ef0a7d655bf">RetentionTime</a>;</div>
<div class="line"><a name="l00060"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TargetedExperiment.html#ad9f8a34047dcd2b9a9f4343b80440d3d">   60</a></span>&#160;    <span class="keyword">typedef</span> <a class="code" href="classOpenMS_1_1TargetedExperimentHelper_1_1Compound.html">TargetedExperimentHelper::Compound</a> <a class="code" href="classOpenMS_1_1TargetedExperiment.html#ad9f8a34047dcd2b9a9f4343b80440d3d">Compound</a>;</div>
<div class="line"><a name="l00061"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TargetedExperiment.html#aa81ff3b563bdf4fff6c1e4e265f2275e">   61</a></span>&#160;    <span class="keyword">typedef</span> <a class="code" href="classOpenMS_1_1TargetedExperimentHelper_1_1Peptide.html">TargetedExperimentHelper::Peptide</a> <a class="code" href="classOpenMS_1_1TargetedExperiment.html#aa81ff3b563bdf4fff6c1e4e265f2275e">Peptide</a>;</div>
<div class="line"><a name="l00062"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TargetedExperiment.html#a8c923cc589e1bc7328743a8cedbe6f75">   62</a></span>&#160;    <span class="keyword">typedef</span> <a class="code" href="structOpenMS_1_1TargetedExperimentHelper_1_1Contact.html">TargetedExperimentHelper::Contact</a> <a class="code" href="classOpenMS_1_1TargetedExperiment.html#a8c923cc589e1bc7328743a8cedbe6f75">Contact</a>;</div>
<div class="line"><a name="l00063"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TargetedExperiment.html#a967776ccb7c71e2110e81a1c50ee8ebd">   63</a></span>&#160;    <span class="keyword">typedef</span> <a class="code" href="structOpenMS_1_1TargetedExperimentHelper_1_1Publication.html">TargetedExperimentHelper::Publication</a> <a class="code" href="classOpenMS_1_1TargetedExperiment.html#a967776ccb7c71e2110e81a1c50ee8ebd">Publication</a>;</div>
<div class="line"><a name="l00064"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TargetedExperiment.html#a43ec2e32ea7ea4fbdb4d7938a53c635f">   64</a></span>&#160;    <span class="keyword">typedef</span> <a class="code" href="structOpenMS_1_1TargetedExperimentHelper_1_1Instrument.html">TargetedExperimentHelper::Instrument</a> <a class="code" href="classOpenMS_1_1TargetedExperiment.html#a43ec2e32ea7ea4fbdb4d7938a53c635f">Instrument</a>;</div>
<div class="line"><a name="l00065"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TargetedExperiment.html#a68ebd15670364c76c9fa8ebcfd725217">   65</a></span>&#160;    <span class="keyword">typedef</span> <a class="code" href="structOpenMS_1_1TargetedExperimentHelper_1_1Prediction.html">TargetedExperimentHelper::Prediction</a> <a class="code" href="classOpenMS_1_1TargetedExperiment.html#a68ebd15670364c76c9fa8ebcfd725217">Prediction</a>;</div>
<div class="line"><a name="l00066"></a><span class="lineno">   66</span>&#160;</div>
<div class="line"><a name="l00067"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TargetedExperiment.html#a0400a7eb8a8d5641172d4f09caa8a18c">   67</a></span>&#160;    <span class="keyword">typedef</span> std::map&lt;String, const Protein *&gt; <a class="code" href="classOpenMS_1_1TargetedExperiment.html#a0400a7eb8a8d5641172d4f09caa8a18c">ProteinReferenceMapType</a>;</div>
<div class="line"><a name="l00068"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TargetedExperiment.html#ad5007e557f54c148146023a446c1cfeb">   68</a></span>&#160;    <span class="keyword">typedef</span> std::map&lt;String, const Peptide *&gt; <a class="code" href="classOpenMS_1_1TargetedExperiment.html#ad5007e557f54c148146023a446c1cfeb">PeptideReferenceMapType</a>;</div>
<div class="line"><a name="l00069"></a><span class="lineno">   69</span>&#160;</div>
<div class="line"><a name="l00073"></a><span class="lineno">   73</span>&#160;    <a class="code" href="classOpenMS_1_1TargetedExperiment.html">TargetedExperiment</a>();</div>
<div class="line"><a name="l00075"></a><span class="lineno">   75</span>&#160;</div>
<div class="line"><a name="l00077"></a><span class="lineno">   77</span>&#160;    <a class="code" href="classOpenMS_1_1TargetedExperiment.html">TargetedExperiment</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1TargetedExperiment.html">TargetedExperiment</a> &amp; rhs);</div>
<div class="line"><a name="l00078"></a><span class="lineno">   78</span>&#160;</div>
<div class="line"><a name="l00080"></a><span class="lineno">   80</span>&#160;    <span class="keyword">virtual</span> ~<a class="code" href="classOpenMS_1_1TargetedExperiment.html">TargetedExperiment</a>();</div>
<div class="line"><a name="l00082"></a><span class="lineno">   82</span>&#160;</div>
<div class="line"><a name="l00084"></a><span class="lineno">   84</span>&#160;    <a class="code" href="classOpenMS_1_1TargetedExperiment.html">TargetedExperiment</a> &amp; operator=(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1TargetedExperiment.html">TargetedExperiment</a> &amp; rhs);</div>
<div class="line"><a name="l00085"></a><span class="lineno">   85</span>&#160;</div>
<div class="line"><a name="l00089"></a><span class="lineno">   89</span>&#160;    <span class="keywordtype">bool</span> operator==(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1TargetedExperiment.html">TargetedExperiment</a> &amp; rhs) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00091"></a><span class="lineno">   91</span>&#160;</div>
<div class="line"><a name="l00097"></a><span class="lineno">   97</span>&#160;    <a class="code" href="classOpenMS_1_1TargetedExperiment.html">TargetedExperiment</a> operator+(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1TargetedExperiment.html">TargetedExperiment</a> &amp; rhs) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00098"></a><span class="lineno">   98</span>&#160;</div>
<div class="line"><a name="l00104"></a><span class="lineno">  104</span>&#160;    <a class="code" href="classOpenMS_1_1TargetedExperiment.html">TargetedExperiment</a> &amp; operator+=(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1TargetedExperiment.html">TargetedExperiment</a> &amp; rhs);</div>
<div class="line"><a name="l00105"></a><span class="lineno">  105</span>&#160;</div>
<div class="line"><a name="l00111"></a><span class="lineno">  111</span>&#160;    <span class="keywordtype">void</span> clear(<span class="keywordtype">bool</span> clear_meta_data);</div>
<div class="line"><a name="l00112"></a><span class="lineno">  112</span>&#160;</div>
<div class="line"><a name="l00116"></a><span class="lineno">  116</span>&#160;    <span class="comment">// cv list</span></div>
<div class="line"><a name="l00117"></a><span class="lineno">  117</span>&#160;    <span class="keywordtype">void</span> setCVs(<span class="keyword">const</span> std::vector&lt;CV&gt; &amp; cvs);</div>
<div class="line"><a name="l00118"></a><span class="lineno">  118</span>&#160;</div>
<div class="line"><a name="l00119"></a><span class="lineno">  119</span>&#160;    <span class="keyword">const</span> std::vector&lt;CV&gt; &amp; getCVs() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00120"></a><span class="lineno">  120</span>&#160;</div>
<div class="line"><a name="l00121"></a><span class="lineno">  121</span>&#160;    <span class="keywordtype">void</span> addCV(<span class="keyword">const</span> <a class="code" href="structOpenMS_1_1TargetedExperimentHelper_1_1CV.html">CV</a> &amp; cv);</div>
<div class="line"><a name="l00122"></a><span class="lineno">  122</span>&#160;</div>
<div class="line"><a name="l00123"></a><span class="lineno">  123</span>&#160;    <span class="comment">// contact list</span></div>
<div class="line"><a name="l00124"></a><span class="lineno">  124</span>&#160;    <span class="keywordtype">void</span> setContacts(<span class="keyword">const</span> std::vector&lt;Contact&gt; &amp; contacts);</div>
<div class="line"><a name="l00125"></a><span class="lineno">  125</span>&#160;</div>
<div class="line"><a name="l00126"></a><span class="lineno">  126</span>&#160;    <span class="keyword">const</span> std::vector&lt;Contact&gt; &amp; getContacts() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00127"></a><span class="lineno">  127</span>&#160;</div>
<div class="line"><a name="l00128"></a><span class="lineno">  128</span>&#160;    <span class="keywordtype">void</span> addContact(<span class="keyword">const</span> <a class="code" href="structOpenMS_1_1TargetedExperimentHelper_1_1Contact.html">Contact</a> &amp; contact);</div>
<div class="line"><a name="l00129"></a><span class="lineno">  129</span>&#160;</div>
<div class="line"><a name="l00130"></a><span class="lineno">  130</span>&#160;    <span class="comment">// publication list</span></div>
<div class="line"><a name="l00131"></a><span class="lineno">  131</span>&#160;    <span class="keywordtype">void</span> setPublications(<span class="keyword">const</span> std::vector&lt;Publication&gt; &amp; publications);</div>
<div class="line"><a name="l00132"></a><span class="lineno">  132</span>&#160;</div>
<div class="line"><a name="l00133"></a><span class="lineno">  133</span>&#160;    <span class="keyword">const</span> std::vector&lt;Publication&gt; &amp; getPublications() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00134"></a><span class="lineno">  134</span>&#160;</div>
<div class="line"><a name="l00135"></a><span class="lineno">  135</span>&#160;    <span class="keywordtype">void</span> addPublication(<span class="keyword">const</span> <a class="code" href="structOpenMS_1_1TargetedExperimentHelper_1_1Publication.html">Publication</a> &amp; publication);</div>
<div class="line"><a name="l00136"></a><span class="lineno">  136</span>&#160;</div>
<div class="line"><a name="l00137"></a><span class="lineno">  137</span>&#160;    <span class="comment">// target list</span></div>
<div class="line"><a name="l00138"></a><span class="lineno">  138</span>&#160;    <span class="keywordtype">void</span> setTargetCVTerms(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1CVTermList.html">CVTermList</a> &amp; cv_terms);</div>
<div class="line"><a name="l00139"></a><span class="lineno">  139</span>&#160;</div>
<div class="line"><a name="l00140"></a><span class="lineno">  140</span>&#160;    <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1CVTermList.html">CVTermList</a> &amp; getTargetCVTerms() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00141"></a><span class="lineno">  141</span>&#160;</div>
<div class="line"><a name="l00142"></a><span class="lineno">  142</span>&#160;    <span class="keywordtype">void</span> addTargetCVTerm(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1CVTerm.html">CVTerm</a> &amp; cv_term);</div>
<div class="line"><a name="l00143"></a><span class="lineno">  143</span>&#160;</div>
<div class="line"><a name="l00144"></a><span class="lineno">  144</span>&#160;    <span class="keywordtype">void</span> setTargetMetaValue(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; name, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1DataValue.html">DataValue</a> &amp; value);</div>
<div class="line"><a name="l00145"></a><span class="lineno">  145</span>&#160;</div>
<div class="line"><a name="l00146"></a><span class="lineno">  146</span>&#160;    <span class="comment">// instrument list</span></div>
<div class="line"><a name="l00147"></a><span class="lineno">  147</span>&#160;    <span class="keywordtype">void</span> setInstruments(<span class="keyword">const</span> std::vector&lt;Instrument&gt; &amp; instruments);</div>
<div class="line"><a name="l00148"></a><span class="lineno">  148</span>&#160;</div>
<div class="line"><a name="l00149"></a><span class="lineno">  149</span>&#160;    <span class="keyword">const</span> std::vector&lt;Instrument&gt; &amp; getInstruments() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00150"></a><span class="lineno">  150</span>&#160;</div>
<div class="line"><a name="l00151"></a><span class="lineno">  151</span>&#160;    <span class="keywordtype">void</span> addInstrument(<span class="keyword">const</span> <a class="code" href="structOpenMS_1_1TargetedExperimentHelper_1_1Instrument.html">Instrument</a> &amp; instrument);</div>
<div class="line"><a name="l00152"></a><span class="lineno">  152</span>&#160;</div>
<div class="line"><a name="l00153"></a><span class="lineno">  153</span>&#160;    <span class="comment">// software list</span></div>
<div class="line"><a name="l00154"></a><span class="lineno">  154</span>&#160;    <span class="keywordtype">void</span> setSoftware(<span class="keyword">const</span> std::vector&lt;Software&gt; &amp; software);</div>
<div class="line"><a name="l00155"></a><span class="lineno">  155</span>&#160;</div>
<div class="line"><a name="l00156"></a><span class="lineno">  156</span>&#160;    <span class="keyword">const</span> std::vector&lt;Software&gt; &amp; getSoftware() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00157"></a><span class="lineno">  157</span>&#160;</div>
<div class="line"><a name="l00158"></a><span class="lineno">  158</span>&#160;    <span class="keywordtype">void</span> addSoftware(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1Software.html">Software</a> &amp; software);</div>
<div class="line"><a name="l00159"></a><span class="lineno">  159</span>&#160;</div>
<div class="line"><a name="l00160"></a><span class="lineno">  160</span>&#160;    <span class="comment">// protein list</span></div>
<div class="line"><a name="l00161"></a><span class="lineno">  161</span>&#160;    <span class="keywordtype">void</span> setProteins(<span class="keyword">const</span> std::vector&lt;Protein&gt; &amp; proteins);</div>
<div class="line"><a name="l00162"></a><span class="lineno">  162</span>&#160;</div>
<div class="line"><a name="l00163"></a><span class="lineno">  163</span>&#160;    <span class="keyword">const</span> std::vector&lt;Protein&gt; &amp; getProteins() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00164"></a><span class="lineno">  164</span>&#160;</div>
<div class="line"><a name="l00165"></a><span class="lineno">  165</span>&#160;    <span class="keyword">const</span> <a class="code" href="structOpenMS_1_1TargetedExperimentHelper_1_1Protein.html">Protein</a> &amp; getProteinByRef(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; ref);</div>
<div class="line"><a name="l00166"></a><span class="lineno">  166</span>&#160;</div>
<div class="line"><a name="l00167"></a><span class="lineno">  167</span>&#160;    <span class="keywordtype">void</span> addProtein(<span class="keyword">const</span> <a class="code" href="structOpenMS_1_1TargetedExperimentHelper_1_1Protein.html">Protein</a> &amp; protein);</div>
<div class="line"><a name="l00168"></a><span class="lineno">  168</span>&#160;</div>
<div class="line"><a name="l00169"></a><span class="lineno">  169</span>&#160;    <span class="comment">// compound list</span></div>
<div class="line"><a name="l00170"></a><span class="lineno">  170</span>&#160;    <span class="keywordtype">void</span> setCompounds(<span class="keyword">const</span> std::vector&lt;Compound&gt; &amp; rhs);</div>
<div class="line"><a name="l00171"></a><span class="lineno">  171</span>&#160;</div>
<div class="line"><a name="l00172"></a><span class="lineno">  172</span>&#160;    <span class="keyword">const</span> std::vector&lt;Compound&gt; &amp; getCompounds() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00173"></a><span class="lineno">  173</span>&#160;</div>
<div class="line"><a name="l00174"></a><span class="lineno">  174</span>&#160;    <span class="keywordtype">void</span> addCompound(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1TargetedExperimentHelper_1_1Compound.html">Compound</a> &amp; rhs);</div>
<div class="line"><a name="l00175"></a><span class="lineno">  175</span>&#160;</div>
<div class="line"><a name="l00176"></a><span class="lineno">  176</span>&#160;    <span class="keywordtype">void</span> setPeptides(<span class="keyword">const</span> std::vector&lt;Peptide&gt; &amp; rhs);</div>
<div class="line"><a name="l00177"></a><span class="lineno">  177</span>&#160;</div>
<div class="line"><a name="l00178"></a><span class="lineno">  178</span>&#160;    <span class="keyword">const</span> std::vector&lt;Peptide&gt; &amp; getPeptides() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00179"></a><span class="lineno">  179</span>&#160;</div>
<div class="line"><a name="l00180"></a><span class="lineno">  180</span>&#160;    <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1TargetedExperimentHelper_1_1Peptide.html">Peptide</a> &amp; getPeptideByRef(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; ref);</div>
<div class="line"><a name="l00181"></a><span class="lineno">  181</span>&#160;</div>
<div class="line"><a name="l00182"></a><span class="lineno">  182</span>&#160;    <span class="keywordtype">void</span> addPeptide(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1TargetedExperimentHelper_1_1Peptide.html">Peptide</a> &amp; rhs);</div>
<div class="line"><a name="l00183"></a><span class="lineno">  183</span>&#160;</div>
<div class="line"><a name="l00185"></a><span class="lineno">  185</span>&#160;    <span class="keywordtype">void</span> setTransitions(<span class="keyword">const</span> std::vector&lt;ReactionMonitoringTransition&gt; &amp; transitions);</div>
<div class="line"><a name="l00186"></a><span class="lineno">  186</span>&#160;</div>
<div class="line"><a name="l00188"></a><span class="lineno">  188</span>&#160;    <span class="keyword">const</span> std::vector&lt;ReactionMonitoringTransition&gt; &amp; getTransitions() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00189"></a><span class="lineno">  189</span>&#160;</div>
<div class="line"><a name="l00191"></a><span class="lineno">  191</span>&#160;    <span class="keywordtype">void</span> addTransition(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ReactionMonitoringTransition.html">ReactionMonitoringTransition</a> &amp; transition);</div>
<div class="line"><a name="l00192"></a><span class="lineno">  192</span>&#160;</div>
<div class="line"><a name="l00193"></a><span class="lineno">  193</span>&#160;    <span class="keywordtype">void</span> setIncludeTargets(<span class="keyword">const</span> std::vector&lt;IncludeExcludeTarget&gt; &amp; targets);</div>
<div class="line"><a name="l00194"></a><span class="lineno">  194</span>&#160;</div>
<div class="line"><a name="l00195"></a><span class="lineno">  195</span>&#160;    <span class="keyword">const</span> std::vector&lt;IncludeExcludeTarget&gt; &amp; getIncludeTargets() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00196"></a><span class="lineno">  196</span>&#160;</div>
<div class="line"><a name="l00197"></a><span class="lineno">  197</span>&#160;    <span class="keywordtype">void</span> addIncludeTarget(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1IncludeExcludeTarget.html">IncludeExcludeTarget</a> &amp; target);</div>
<div class="line"><a name="l00198"></a><span class="lineno">  198</span>&#160;</div>
<div class="line"><a name="l00199"></a><span class="lineno">  199</span>&#160;    <span class="keywordtype">void</span> setExcludeTargets(<span class="keyword">const</span> std::vector&lt;IncludeExcludeTarget&gt; &amp; targets);</div>
<div class="line"><a name="l00200"></a><span class="lineno">  200</span>&#160;</div>
<div class="line"><a name="l00201"></a><span class="lineno">  201</span>&#160;    <span class="keyword">const</span> std::vector&lt;IncludeExcludeTarget&gt; &amp; getExcludeTargets() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00202"></a><span class="lineno">  202</span>&#160;</div>
<div class="line"><a name="l00203"></a><span class="lineno">  203</span>&#160;    <span class="keywordtype">void</span> addExcludeTarget(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1IncludeExcludeTarget.html">IncludeExcludeTarget</a> &amp; target);</div>
<div class="line"><a name="l00204"></a><span class="lineno">  204</span>&#160;</div>
<div class="line"><a name="l00206"></a><span class="lineno">  206</span>&#160;    <span class="keywordtype">void</span> setSourceFiles(<span class="keyword">const</span> std::vector&lt;SourceFile&gt; &amp; source_files);</div>
<div class="line"><a name="l00207"></a><span class="lineno">  207</span>&#160;</div>
<div class="line"><a name="l00209"></a><span class="lineno">  209</span>&#160;    <span class="keyword">const</span> std::vector&lt;SourceFile&gt; &amp; getSourceFiles() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00210"></a><span class="lineno">  210</span>&#160;</div>
<div class="line"><a name="l00212"></a><span class="lineno">  212</span>&#160;    <span class="keywordtype">void</span> addSourceFile(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1SourceFile.html">SourceFile</a> &amp; source_file);</div>
<div class="line"><a name="l00214"></a><span class="lineno">  214</span>&#160;</div>
<div class="line"><a name="l00216"></a><span class="lineno">  216</span>&#160;</div>
<div class="line"><a name="l00217"></a><span class="lineno">  217</span>&#160;</div>
<div class="line"><a name="l00220"></a><span class="lineno">  220</span>&#160;    <span class="keywordtype">void</span> sortTransitionsByProductMZ();</div>
<div class="line"><a name="l00222"></a><span class="lineno">  222</span>&#160;</div>
<div class="line"><a name="l00223"></a><span class="lineno">  223</span>&#160;<span class="keyword">protected</span>:</div>
<div class="line"><a name="l00224"></a><span class="lineno">  224</span>&#160;</div>
<div class="line"><a name="l00225"></a><span class="lineno">  225</span>&#160;    <span class="keywordtype">void</span> createProteinReferenceMap_();</div>
<div class="line"><a name="l00226"></a><span class="lineno">  226</span>&#160;</div>
<div class="line"><a name="l00227"></a><span class="lineno">  227</span>&#160;    <span class="keywordtype">void</span> createPeptideReferenceMap_();</div>
<div class="line"><a name="l00228"></a><span class="lineno">  228</span>&#160;</div>
<div class="line"><a name="l00229"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TargetedExperiment.html#a52f2af20740218faa4933b7d1617cf96">  229</a></span>&#160;    std::vector&lt;CV&gt; <a class="code" href="classOpenMS_1_1TargetedExperiment.html#a52f2af20740218faa4933b7d1617cf96">cvs_</a>;</div>
<div class="line"><a name="l00230"></a><span class="lineno">  230</span>&#160;</div>
<div class="line"><a name="l00231"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TargetedExperiment.html#a1de02993eba2d1ce1f8ec9e06ea28e9e">  231</a></span>&#160;    std::vector&lt;Contact&gt; <a class="code" href="classOpenMS_1_1TargetedExperiment.html#a1de02993eba2d1ce1f8ec9e06ea28e9e">contacts_</a>;</div>
<div class="line"><a name="l00232"></a><span class="lineno">  232</span>&#160;</div>
<div class="line"><a name="l00233"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TargetedExperiment.html#abb5b9e36128aa8a944c25385400d8878">  233</a></span>&#160;    std::vector&lt;Publication&gt; <a class="code" href="classOpenMS_1_1TargetedExperiment.html#abb5b9e36128aa8a944c25385400d8878">publications_</a>;</div>
<div class="line"><a name="l00234"></a><span class="lineno">  234</span>&#160;</div>
<div class="line"><a name="l00235"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TargetedExperiment.html#a94d31162aa7b7a0d5e405c204572a697">  235</a></span>&#160;    std::vector&lt;Instrument&gt; <a class="code" href="classOpenMS_1_1TargetedExperiment.html#a94d31162aa7b7a0d5e405c204572a697">instruments_</a>;</div>
<div class="line"><a name="l00236"></a><span class="lineno">  236</span>&#160;</div>
<div class="line"><a name="l00237"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TargetedExperiment.html#a221e5a78a25ae13b2cfe9b4f2caeadb8">  237</a></span>&#160;    <a class="code" href="classOpenMS_1_1CVTermList.html">CVTermList</a> <a class="code" href="classOpenMS_1_1TargetedExperiment.html#a221e5a78a25ae13b2cfe9b4f2caeadb8">targets_</a>;</div>
<div class="line"><a name="l00238"></a><span class="lineno">  238</span>&#160;</div>
<div class="line"><a name="l00239"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TargetedExperiment.html#ad67105887a305fbd0345cadb468a957b">  239</a></span>&#160;    std::vector&lt;Software&gt; <a class="code" href="classOpenMS_1_1TargetedExperiment.html#ad67105887a305fbd0345cadb468a957b">software_</a>;</div>
<div class="line"><a name="l00240"></a><span class="lineno">  240</span>&#160;</div>
<div class="line"><a name="l00241"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TargetedExperiment.html#ab2d08be0f1ac103d135c8031c340a946">  241</a></span>&#160;    std::vector&lt;Protein&gt; <a class="code" href="classOpenMS_1_1TargetedExperiment.html#ab2d08be0f1ac103d135c8031c340a946">proteins_</a>;</div>
<div class="line"><a name="l00242"></a><span class="lineno">  242</span>&#160;</div>
<div class="line"><a name="l00243"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TargetedExperiment.html#a7daeb46f15f205b6f970d3117f3e3e69">  243</a></span>&#160;    std::vector&lt;Compound&gt; <a class="code" href="classOpenMS_1_1TargetedExperiment.html#a7daeb46f15f205b6f970d3117f3e3e69">compounds_</a>;</div>
<div class="line"><a name="l00244"></a><span class="lineno">  244</span>&#160;</div>
<div class="line"><a name="l00245"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TargetedExperiment.html#a748a750efa2c7114ea34f16e0742c5a7">  245</a></span>&#160;    std::vector&lt;Peptide&gt; <a class="code" href="classOpenMS_1_1TargetedExperiment.html#a748a750efa2c7114ea34f16e0742c5a7">peptides_</a>;</div>
<div class="line"><a name="l00246"></a><span class="lineno">  246</span>&#160;</div>
<div class="line"><a name="l00247"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TargetedExperiment.html#abb0eb582391f4fb009828c771881496b">  247</a></span>&#160;    std::vector&lt;ReactionMonitoringTransition&gt; <a class="code" href="classOpenMS_1_1TargetedExperiment.html#abb0eb582391f4fb009828c771881496b">transitions_</a>;</div>
<div class="line"><a name="l00248"></a><span class="lineno">  248</span>&#160;</div>
<div class="line"><a name="l00249"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TargetedExperiment.html#a9b995e0c16c83555953a18d4aff2161e">  249</a></span>&#160;    std::vector&lt;IncludeExcludeTarget&gt; <a class="code" href="classOpenMS_1_1TargetedExperiment.html#a9b995e0c16c83555953a18d4aff2161e">include_targets_</a>;</div>
<div class="line"><a name="l00250"></a><span class="lineno">  250</span>&#160;</div>
<div class="line"><a name="l00251"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TargetedExperiment.html#aa5f7f2226e6d7f8f046536d7ccb5225e">  251</a></span>&#160;    std::vector&lt;IncludeExcludeTarget&gt; <a class="code" href="classOpenMS_1_1TargetedExperiment.html#aa5f7f2226e6d7f8f046536d7ccb5225e">exclude_targets_</a>;</div>
<div class="line"><a name="l00252"></a><span class="lineno">  252</span>&#160;</div>
<div class="line"><a name="l00253"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TargetedExperiment.html#a72a82b25931a7ecc3444b375069ca892">  253</a></span>&#160;    std::vector&lt;SourceFile&gt; <a class="code" href="classOpenMS_1_1TargetedExperiment.html#a72a82b25931a7ecc3444b375069ca892">source_files_</a>;</div>
<div class="line"><a name="l00254"></a><span class="lineno">  254</span>&#160;</div>
<div class="line"><a name="l00255"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TargetedExperiment.html#a9d74d4a5d7c9a776c5afbb9628fbc3d5">  255</a></span>&#160;    <a class="code" href="classOpenMS_1_1TargetedExperiment.html#a0400a7eb8a8d5641172d4f09caa8a18c">ProteinReferenceMapType</a> <a class="code" href="classOpenMS_1_1TargetedExperiment.html#a9d74d4a5d7c9a776c5afbb9628fbc3d5">protein_reference_map_</a>;</div>
<div class="line"><a name="l00256"></a><span class="lineno">  256</span>&#160;</div>
<div class="line"><a name="l00257"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TargetedExperiment.html#acd439a955b648ba43bdc8c5daf5bce99">  257</a></span>&#160;    <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1TargetedExperiment.html#acd439a955b648ba43bdc8c5daf5bce99">protein_reference_map_dirty_</a>;</div>
<div class="line"><a name="l00258"></a><span class="lineno">  258</span>&#160;</div>
<div class="line"><a name="l00259"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TargetedExperiment.html#adcbe3c4030a97e978bd547928bf71d9e">  259</a></span>&#160;    <a class="code" href="classOpenMS_1_1TargetedExperiment.html#ad5007e557f54c148146023a446c1cfeb">PeptideReferenceMapType</a> <a class="code" href="classOpenMS_1_1TargetedExperiment.html#adcbe3c4030a97e978bd547928bf71d9e">peptide_reference_map_</a>;</div>
<div class="line"><a name="l00260"></a><span class="lineno">  260</span>&#160;</div>
<div class="line"><a name="l00261"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TargetedExperiment.html#afc3f7fca733362e91a2bb91afc26e9e0">  261</a></span>&#160;    <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1TargetedExperiment.html#afc3f7fca733362e91a2bb91afc26e9e0">peptide_reference_map_dirty_</a>;</div>
<div class="line"><a name="l00262"></a><span class="lineno">  262</span>&#160;</div>
<div class="line"><a name="l00263"></a><span class="lineno">  263</span>&#160;  };</div>
<div class="line"><a name="l00264"></a><span class="lineno">  264</span>&#160;</div>
<div class="line"><a name="l00265"></a><span class="lineno">  265</span>&#160;</div>
<div class="line"><a name="l00266"></a><span class="lineno"><a class="line" href="namespaceOpenMS_1_1TargetedExperimentHelper.html">  266</a></span>&#160;  <span class="keyword">namespace </span>TargetedExperimentHelper</div>
<div class="line"><a name="l00267"></a><span class="lineno">  267</span>&#160;  {</div>
<div class="line"><a name="l00268"></a><span class="lineno">  268</span>&#160;  } <span class="comment">// namespace TargetedExperimentHelper</span></div>
<div class="line"><a name="l00269"></a><span class="lineno">  269</span>&#160;</div>
<div class="line"><a name="l00270"></a><span class="lineno">  270</span>&#160;</div>
<div class="line"><a name="l00271"></a><span class="lineno">  271</span>&#160;} <span class="comment">// namespace OpenMS</span></div>
<div class="line"><a name="l00272"></a><span class="lineno">  272</span>&#160;</div>
<div class="line"><a name="l00273"></a><span class="lineno">  273</span>&#160;<span class="preprocessor">#endif // OPENMS_ANALYSIS_TARGETED_TARGETEDEXPERIMENT_H</span></div>
<div class="ttc" id="TargetedExperimentHelper_8h_html"><div class="ttname"><a href="TargetedExperimentHelper_8h.html">TargetedExperimentHelper.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1TargetedExperiment_html_a221e5a78a25ae13b2cfe9b4f2caeadb8"><div class="ttname"><a href="classOpenMS_1_1TargetedExperiment.html#a221e5a78a25ae13b2cfe9b4f2caeadb8">OpenMS::TargetedExperiment::targets_</a></div><div class="ttdeci">CVTermList targets_</div><div class="ttdef"><b>Definition:</b> TargetedExperiment.h:237</div></div>
<div class="ttc" id="CVTermList_8h_html"><div class="ttname"><a href="CVTermList_8h.html">CVTermList.h</a></div></div>
<div class="ttc" id="StandardTypes_8h_html"><div class="ttname"><a href="StandardTypes_8h.html">StandardTypes.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1String_html"><div class="ttname"><a href="classOpenMS_1_1String.html">OpenMS::String</a></div><div class="ttdoc">A more convenient string class. </div><div class="ttdef"><b>Definition:</b> String.h:56</div></div>
<div class="ttc" id="classOpenMS_1_1TargetedExperiment_html_a9b995e0c16c83555953a18d4aff2161e"><div class="ttname"><a href="classOpenMS_1_1TargetedExperiment.html#a9b995e0c16c83555953a18d4aff2161e">OpenMS::TargetedExperiment::include_targets_</a></div><div class="ttdeci">std::vector&lt; IncludeExcludeTarget &gt; include_targets_</div><div class="ttdef"><b>Definition:</b> TargetedExperiment.h:249</div></div>
<div class="ttc" id="classOpenMS_1_1CVTermList_html"><div class="ttname"><a href="classOpenMS_1_1CVTermList.html">OpenMS::CVTermList</a></div><div class="ttdoc">Representation of controlled vocabulary term list. </div><div class="ttdef"><b>Definition:</b> CVTermList.h:54</div></div>
<div class="ttc" id="Software_8h_html"><div class="ttname"><a href="Software_8h.html">Software.h</a></div></div>
<div class="ttc" id="structOpenMS_1_1TargetedExperimentHelper_1_1Publication_html"><div class="ttname"><a href="structOpenMS_1_1TargetedExperimentHelper_1_1Publication.html">OpenMS::TargetedExperimentHelper::Publication</a></div><div class="ttdef"><b>Definition:</b> TargetedExperimentHelper.h:374</div></div>
<div class="ttc" id="classOpenMS_1_1TargetedExperiment_html_aa81ff3b563bdf4fff6c1e4e265f2275e"><div class="ttname"><a href="classOpenMS_1_1TargetedExperiment.html#aa81ff3b563bdf4fff6c1e4e265f2275e">OpenMS::TargetedExperiment::Peptide</a></div><div class="ttdeci">TargetedExperimentHelper::Peptide Peptide</div><div class="ttdef"><b>Definition:</b> TargetedExperiment.h:61</div></div>
<div class="ttc" id="classOpenMS_1_1TargetedExperiment_html_a9d74d4a5d7c9a776c5afbb9628fbc3d5"><div class="ttname"><a href="classOpenMS_1_1TargetedExperiment.html#a9d74d4a5d7c9a776c5afbb9628fbc3d5">OpenMS::TargetedExperiment::protein_reference_map_</a></div><div class="ttdeci">ProteinReferenceMapType protein_reference_map_</div><div class="ttdef"><b>Definition:</b> TargetedExperiment.h:255</div></div>
<div class="ttc" id="classOpenMS_1_1TargetedExperiment_html_ab2d08be0f1ac103d135c8031c340a946"><div class="ttname"><a href="classOpenMS_1_1TargetedExperiment.html#ab2d08be0f1ac103d135c8031c340a946">OpenMS::TargetedExperiment::proteins_</a></div><div class="ttdeci">std::vector&lt; Protein &gt; proteins_</div><div class="ttdef"><b>Definition:</b> TargetedExperiment.h:241</div></div>
<div class="ttc" id="classOpenMS_1_1SourceFile_html"><div class="ttname"><a href="classOpenMS_1_1SourceFile.html">OpenMS::SourceFile</a></div><div class="ttdoc">Description of a file location, used to store the origin of (meta) data. </div><div class="ttdef"><b>Definition:</b> SourceFile.h:47</div></div>
<div class="ttc" id="classOpenMS_1_1TargetedExperiment_html_a748a750efa2c7114ea34f16e0742c5a7"><div class="ttname"><a href="classOpenMS_1_1TargetedExperiment.html#a748a750efa2c7114ea34f16e0742c5a7">OpenMS::TargetedExperiment::peptides_</a></div><div class="ttdeci">std::vector&lt; Peptide &gt; peptides_</div><div class="ttdef"><b>Definition:</b> TargetedExperiment.h:245</div></div>
<div class="ttc" id="structOpenMS_1_1TargetedExperimentHelper_1_1Contact_html"><div class="ttname"><a href="structOpenMS_1_1TargetedExperimentHelper_1_1Contact.html">OpenMS::TargetedExperimentHelper::Contact</a></div><div class="ttdef"><b>Definition:</b> TargetedExperimentHelper.h:346</div></div>
<div class="ttc" id="classOpenMS_1_1Software_html"><div class="ttname"><a href="classOpenMS_1_1Software.html">OpenMS::Software</a></div><div class="ttdoc">Description of the software used for processing. </div><div class="ttdef"><b>Definition:</b> Software.h:49</div></div>
<div class="ttc" id="classOpenMS_1_1DataValue_html"><div class="ttname"><a href="classOpenMS_1_1DataValue.html">OpenMS::DataValue</a></div><div class="ttdoc">Class to hold strings, numeric values, lists of strings and lists of numeric values. </div><div class="ttdef"><b>Definition:</b> DataValue.h:57</div></div>
<div class="ttc" id="classOpenMS_1_1TargetedExperiment_html_afc3f7fca733362e91a2bb91afc26e9e0"><div class="ttname"><a href="classOpenMS_1_1TargetedExperiment.html#afc3f7fca733362e91a2bb91afc26e9e0">OpenMS::TargetedExperiment::peptide_reference_map_dirty_</a></div><div class="ttdeci">bool peptide_reference_map_dirty_</div><div class="ttdef"><b>Definition:</b> TargetedExperiment.h:261</div></div>
<div class="ttc" id="classOpenMS_1_1TargetedExperiment_html_a72a82b25931a7ecc3444b375069ca892"><div class="ttname"><a href="classOpenMS_1_1TargetedExperiment.html#a72a82b25931a7ecc3444b375069ca892">OpenMS::TargetedExperiment::source_files_</a></div><div class="ttdeci">std::vector&lt; SourceFile &gt; source_files_</div><div class="ttdef"><b>Definition:</b> TargetedExperiment.h:253</div></div>
<div class="ttc" id="classOpenMS_1_1TargetedExperiment_html_a7daeb46f15f205b6f970d3117f3e3e69"><div class="ttname"><a href="classOpenMS_1_1TargetedExperiment.html#a7daeb46f15f205b6f970d3117f3e3e69">OpenMS::TargetedExperiment::compounds_</a></div><div class="ttdeci">std::vector&lt; Compound &gt; compounds_</div><div class="ttdef"><b>Definition:</b> TargetedExperiment.h:243</div></div>
<div class="ttc" id="classOpenMS_1_1TargetedExperiment_html_ad5007e557f54c148146023a446c1cfeb"><div class="ttname"><a href="classOpenMS_1_1TargetedExperiment.html#ad5007e557f54c148146023a446c1cfeb">OpenMS::TargetedExperiment::PeptideReferenceMapType</a></div><div class="ttdeci">std::map&lt; String, const Peptide * &gt; PeptideReferenceMapType</div><div class="ttdef"><b>Definition:</b> TargetedExperiment.h:68</div></div>
<div class="ttc" id="classOpenMS_1_1TargetedExperiment_html_a1de02993eba2d1ce1f8ec9e06ea28e9e"><div class="ttname"><a href="classOpenMS_1_1TargetedExperiment.html#a1de02993eba2d1ce1f8ec9e06ea28e9e">OpenMS::TargetedExperiment::contacts_</a></div><div class="ttdeci">std::vector&lt; Contact &gt; contacts_</div><div class="ttdef"><b>Definition:</b> TargetedExperiment.h:231</div></div>
<div class="ttc" id="classOpenMS_1_1TargetedExperiment_html_a94d31162aa7b7a0d5e405c204572a697"><div class="ttname"><a href="classOpenMS_1_1TargetedExperiment.html#a94d31162aa7b7a0d5e405c204572a697">OpenMS::TargetedExperiment::instruments_</a></div><div class="ttdeci">std::vector&lt; Instrument &gt; instruments_</div><div class="ttdef"><b>Definition:</b> TargetedExperiment.h:235</div></div>
<div class="ttc" id="classOpenMS_1_1TargetedExperiment_html_a68ebd15670364c76c9fa8ebcfd725217"><div class="ttname"><a href="classOpenMS_1_1TargetedExperiment.html#a68ebd15670364c76c9fa8ebcfd725217">OpenMS::TargetedExperiment::Prediction</a></div><div class="ttdeci">TargetedExperimentHelper::Prediction Prediction</div><div class="ttdef"><b>Definition:</b> TargetedExperiment.h:65</div></div>
<div class="ttc" id="classOpenMS_1_1TargetedExperiment_html_a6be5011e53737493e15d175f5d4a1d03"><div class="ttname"><a href="classOpenMS_1_1TargetedExperiment.html#a6be5011e53737493e15d175f5d4a1d03">OpenMS::TargetedExperiment::Protein</a></div><div class="ttdeci">TargetedExperimentHelper::Protein Protein</div><div class="ttdef"><b>Definition:</b> TargetedExperiment.h:58</div></div>
<div class="ttc" id="classOpenMS_1_1CVTerm_html"><div class="ttname"><a href="classOpenMS_1_1CVTerm.html">OpenMS::CVTerm</a></div><div class="ttdoc">Representation of controlled vocabulary term. </div><div class="ttdef"><b>Definition:</b> CVTerm.h:51</div></div>
<div class="ttc" id="classOpenMS_1_1TargetedExperiment_html_a52f2af20740218faa4933b7d1617cf96"><div class="ttname"><a href="classOpenMS_1_1TargetedExperiment.html#a52f2af20740218faa4933b7d1617cf96">OpenMS::TargetedExperiment::cvs_</a></div><div class="ttdeci">std::vector&lt; CV &gt; cvs_</div><div class="ttdef"><b>Definition:</b> TargetedExperiment.h:229</div></div>
<div class="ttc" id="classOpenMS_1_1TargetedExperimentHelper_1_1Compound_html"><div class="ttname"><a href="classOpenMS_1_1TargetedExperimentHelper_1_1Compound.html">OpenMS::TargetedExperimentHelper::Compound</a></div><div class="ttdef"><b>Definition:</b> TargetedExperimentHelper.h:172</div></div>
<div class="ttc" id="classOpenMS_1_1TargetedExperiment_html_a0400a7eb8a8d5641172d4f09caa8a18c"><div class="ttname"><a href="classOpenMS_1_1TargetedExperiment.html#a0400a7eb8a8d5641172d4f09caa8a18c">OpenMS::TargetedExperiment::ProteinReferenceMapType</a></div><div class="ttdeci">std::map&lt; String, const Protein * &gt; ProteinReferenceMapType</div><div class="ttdef"><b>Definition:</b> TargetedExperiment.h:67</div></div>
<div class="ttc" id="classOpenMS_1_1TargetedExperiment_html_acd439a955b648ba43bdc8c5daf5bce99"><div class="ttname"><a href="classOpenMS_1_1TargetedExperiment.html#acd439a955b648ba43bdc8c5daf5bce99">OpenMS::TargetedExperiment::protein_reference_map_dirty_</a></div><div class="ttdeci">bool protein_reference_map_dirty_</div><div class="ttdef"><b>Definition:</b> TargetedExperiment.h:257</div></div>
<div class="ttc" id="structOpenMS_1_1TargetedExperimentHelper_1_1CV_html"><div class="ttname"><a href="structOpenMS_1_1TargetedExperimentHelper_1_1CV.html">OpenMS::TargetedExperimentHelper::CV</a></div><div class="ttdef"><b>Definition:</b> TargetedExperimentHelper.h:76</div></div>
<div class="ttc" id="classOpenMS_1_1IncludeExcludeTarget_html"><div class="ttname"><a href="classOpenMS_1_1IncludeExcludeTarget.html">OpenMS::IncludeExcludeTarget</a></div><div class="ttdoc">This class stores a SRM/MRM transition. </div><div class="ttdef"><b>Definition:</b> IncludeExcludeTarget.h:53</div></div>
<div class="ttc" id="classOpenMS_1_1TargetedExperiment_html_abb0eb582391f4fb009828c771881496b"><div class="ttname"><a href="classOpenMS_1_1TargetedExperiment.html#abb0eb582391f4fb009828c771881496b">OpenMS::TargetedExperiment::transitions_</a></div><div class="ttdeci">std::vector&lt; ReactionMonitoringTransition &gt; transitions_</div><div class="ttdef"><b>Definition:</b> TargetedExperiment.h:247</div></div>
<div class="ttc" id="classOpenMS_1_1TargetedExperiment_html_adcbe3c4030a97e978bd547928bf71d9e"><div class="ttname"><a href="classOpenMS_1_1TargetedExperiment.html#adcbe3c4030a97e978bd547928bf71d9e">OpenMS::TargetedExperiment::peptide_reference_map_</a></div><div class="ttdeci">PeptideReferenceMapType peptide_reference_map_</div><div class="ttdef"><b>Definition:</b> TargetedExperiment.h:259</div></div>
<div class="ttc" id="classOpenMS_1_1TargetedExperiment_html_aa5f7f2226e6d7f8f046536d7ccb5225e"><div class="ttname"><a href="classOpenMS_1_1TargetedExperiment.html#aa5f7f2226e6d7f8f046536d7ccb5225e">OpenMS::TargetedExperiment::exclude_targets_</a></div><div class="ttdeci">std::vector&lt; IncludeExcludeTarget &gt; exclude_targets_</div><div class="ttdef"><b>Definition:</b> TargetedExperiment.h:251</div></div>
<div class="ttc" id="CVTerm_8h_html"><div class="ttname"><a href="CVTerm_8h.html">CVTerm.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1TargetedExperiment_html"><div class="ttname"><a href="classOpenMS_1_1TargetedExperiment.html">OpenMS::TargetedExperiment</a></div><div class="ttdoc">This class stores an prediction of an SRM/MRM transition. </div><div class="ttdef"><b>Definition:</b> TargetedExperiment.h:53</div></div>
<div class="ttc" id="structOpenMS_1_1TargetedExperimentHelper_1_1Instrument_html"><div class="ttname"><a href="structOpenMS_1_1TargetedExperimentHelper_1_1Instrument.html">OpenMS::TargetedExperimentHelper::Instrument</a></div><div class="ttdef"><b>Definition:</b> TargetedExperimentHelper.h:402</div></div>
<div class="ttc" id="classOpenMS_1_1TargetedExperimentHelper_1_1RetentionTime_html"><div class="ttname"><a href="classOpenMS_1_1TargetedExperimentHelper_1_1RetentionTime.html">OpenMS::TargetedExperimentHelper::RetentionTime</a></div><div class="ttdef"><b>Definition:</b> TargetedExperimentHelper.h:133</div></div>
<div class="ttc" id="classOpenMS_1_1TargetedExperiment_html_a43ec2e32ea7ea4fbdb4d7938a53c635f"><div class="ttname"><a href="classOpenMS_1_1TargetedExperiment.html#a43ec2e32ea7ea4fbdb4d7938a53c635f">OpenMS::TargetedExperiment::Instrument</a></div><div class="ttdeci">TargetedExperimentHelper::Instrument Instrument</div><div class="ttdef"><b>Definition:</b> TargetedExperiment.h:64</div></div>
<div class="ttc" id="structOpenMS_1_1TargetedExperimentHelper_1_1Prediction_html"><div class="ttname"><a href="structOpenMS_1_1TargetedExperimentHelper_1_1Prediction.html">OpenMS::TargetedExperimentHelper::Prediction</a></div><div class="ttdef"><b>Definition:</b> TargetedExperimentHelper.h:430</div></div>
<div class="ttc" id="classOpenMS_1_1TargetedExperiment_html_ad67105887a305fbd0345cadb468a957b"><div class="ttname"><a href="classOpenMS_1_1TargetedExperiment.html#ad67105887a305fbd0345cadb468a957b">OpenMS::TargetedExperiment::software_</a></div><div class="ttdeci">std::vector&lt; Software &gt; software_</div><div class="ttdef"><b>Definition:</b> TargetedExperiment.h:239</div></div>
<div class="ttc" id="classOpenMS_1_1TargetedExperiment_html_a967776ccb7c71e2110e81a1c50ee8ebd"><div class="ttname"><a href="classOpenMS_1_1TargetedExperiment.html#a967776ccb7c71e2110e81a1c50ee8ebd">OpenMS::TargetedExperiment::Publication</a></div><div class="ttdeci">TargetedExperimentHelper::Publication Publication</div><div class="ttdef"><b>Definition:</b> TargetedExperiment.h:63</div></div>
<div class="ttc" id="structOpenMS_1_1TargetedExperimentHelper_1_1Protein_html"><div class="ttname"><a href="structOpenMS_1_1TargetedExperimentHelper_1_1Protein.html">OpenMS::TargetedExperimentHelper::Protein</a></div><div class="ttdef"><b>Definition:</b> TargetedExperimentHelper.h:102</div></div>
<div class="ttc" id="IncludeExcludeTarget_8h_html"><div class="ttname"><a href="IncludeExcludeTarget_8h.html">IncludeExcludeTarget.h</a></div></div>
<div class="ttc" id="ReactionMonitoringTransition_8h_html"><div class="ttname"><a href="ReactionMonitoringTransition_8h.html">ReactionMonitoringTransition.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1TargetedExperiment_html_a8c923cc589e1bc7328743a8cedbe6f75"><div class="ttname"><a href="classOpenMS_1_1TargetedExperiment.html#a8c923cc589e1bc7328743a8cedbe6f75">OpenMS::TargetedExperiment::Contact</a></div><div class="ttdeci">TargetedExperimentHelper::Contact Contact</div><div class="ttdef"><b>Definition:</b> TargetedExperiment.h:62</div></div>
<div class="ttc" id="classOpenMS_1_1TargetedExperiment_html_ad9f8a34047dcd2b9a9f4343b80440d3d"><div class="ttname"><a href="classOpenMS_1_1TargetedExperiment.html#ad9f8a34047dcd2b9a9f4343b80440d3d">OpenMS::TargetedExperiment::Compound</a></div><div class="ttdeci">TargetedExperimentHelper::Compound Compound</div><div class="ttdef"><b>Definition:</b> TargetedExperiment.h:60</div></div>
<div class="ttc" id="classOpenMS_1_1TargetedExperiment_html_abb5b9e36128aa8a944c25385400d8878"><div class="ttname"><a href="classOpenMS_1_1TargetedExperiment.html#abb5b9e36128aa8a944c25385400d8878">OpenMS::TargetedExperiment::publications_</a></div><div class="ttdeci">std::vector&lt; Publication &gt; publications_</div><div class="ttdef"><b>Definition:</b> TargetedExperiment.h:233</div></div>
<div class="ttc" id="classOpenMS_1_1TargetedExperiment_html_abd581285516dfa4bdd8753a5568931d3"><div class="ttname"><a href="classOpenMS_1_1TargetedExperiment.html#abd581285516dfa4bdd8753a5568931d3">OpenMS::TargetedExperiment::CV</a></div><div class="ttdeci">TargetedExperimentHelper::CV CV</div><div class="ttdef"><b>Definition:</b> TargetedExperiment.h:57</div></div>
<div class="ttc" id="classOpenMS_1_1TargetedExperimentHelper_1_1Peptide_html"><div class="ttname"><a href="classOpenMS_1_1TargetedExperimentHelper_1_1Peptide.html">OpenMS::TargetedExperimentHelper::Peptide</a></div><div class="ttdef"><b>Definition:</b> TargetedExperimentHelper.h:211</div></div>
<div class="ttc" id="classOpenMS_1_1ReactionMonitoringTransition_html"><div class="ttname"><a href="classOpenMS_1_1ReactionMonitoringTransition.html">OpenMS::ReactionMonitoringTransition</a></div><div class="ttdoc">This class stores a SRM/MRM transition. </div><div class="ttdef"><b>Definition:</b> ReactionMonitoringTransition.h:53</div></div>
<div class="ttc" id="classOpenMS_1_1TargetedExperiment_html_aecbf6dcfb8bc066ff62e1ef0a7d655bf"><div class="ttname"><a href="classOpenMS_1_1TargetedExperiment.html#aecbf6dcfb8bc066ff62e1ef0a7d655bf">OpenMS::TargetedExperiment::RetentionTime</a></div><div class="ttdeci">TargetedExperimentHelper::RetentionTime RetentionTime</div><div class="ttdef"><b>Definition:</b> TargetedExperiment.h:59</div></div>
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