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<a href="TraMLHandler_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, Hannes Roest $</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_FORMAT_HANDLERS_TRAMLHANDLER_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_FORMAT_HANDLERS_TRAMLHANDLER_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="XMLHandler_8h.html">OpenMS/FORMAT/HANDLERS/XMLHandler.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="ControlledVocabulary_8h.html">OpenMS/FORMAT/ControlledVocabulary.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="TargetedExperiment_8h.html">OpenMS/ANALYSIS/TARGETED/TargetedExperiment.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="CVTermList_8h.html">OpenMS/METADATA/CVTermList.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="ProgressLogger_8h.html">OpenMS/CONCEPT/ProgressLogger.h</a>&gt;</span></div>
<div class="line"><a name="l00043"></a><span class="lineno">   43</span>&#160;</div>
<div class="line"><a name="l00044"></a><span class="lineno">   44</span>&#160;<span class="keyword">namespace </span>OpenMS</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="keyword">namespace </span>Internal</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;</div>
<div class="line"><a name="l00054"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1TraMLHandler.html">   54</a></span>&#160;    <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1Internal_1_1TraMLHandler.html">TraMLHandler</a> :</div>
<div class="line"><a name="l00055"></a><span class="lineno">   55</span>&#160;      <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1Internal_1_1XMLHandler.html">XMLHandler</a></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">   57</span>&#160;<span class="keyword">public</span>:</div>
<div class="line"><a name="l00058"></a><span class="lineno">   58</span>&#160;</div>
<div class="line"><a name="l00059"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1TraMLHandler.html#a50ebcf434b59ba84992d03316e3a1628">   59</a></span>&#160;      <span class="keyword">typedef</span> std::vector&lt;ReactionMonitoringTransition::Product&gt; <a class="code" href="classOpenMS_1_1Internal_1_1TraMLHandler.html#a50ebcf434b59ba84992d03316e3a1628">ProductListType</a>;</div>
<div class="line"><a name="l00060"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1TraMLHandler.html#a12660f60dd5d2eb3fe66e2c819199465">   60</a></span>&#160;      <span class="keyword">typedef</span> std::vector&lt;ReactionMonitoringTransition::Configuration&gt; <a class="code" href="classOpenMS_1_1Internal_1_1TraMLHandler.html#a12660f60dd5d2eb3fe66e2c819199465">ConfigurationListType</a>;</div>
<div class="line"><a name="l00061"></a><span class="lineno">   61</span>&#160;</div>
<div class="line"><a name="l00064"></a><span class="lineno">   64</span>&#160;      <a class="code" href="classOpenMS_1_1Internal_1_1TraMLHandler.html">TraMLHandler</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1TargetedExperiment.html">TargetedExperiment</a> &amp; exp, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; filename, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; version, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a> &amp; logger);</div>
<div class="line"><a name="l00066"></a><span class="lineno">   66</span>&#160;</div>
<div class="line"><a name="l00068"></a><span class="lineno">   68</span>&#160;      <a class="code" href="classOpenMS_1_1Internal_1_1TraMLHandler.html">TraMLHandler</a>(<a class="code" href="classOpenMS_1_1TargetedExperiment.html">TargetedExperiment</a> &amp; exp, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; filename, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; version, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a> &amp; logger);</div>
<div class="line"><a name="l00069"></a><span class="lineno">   69</span>&#160;</div>
<div class="line"><a name="l00071"></a><span class="lineno">   71</span>&#160;      <span class="keyword">virtual</span> ~<a class="code" href="classOpenMS_1_1Internal_1_1TraMLHandler.html">TraMLHandler</a>();</div>
<div class="line"><a name="l00073"></a><span class="lineno">   73</span>&#160;</div>
<div class="line"><a name="l00074"></a><span class="lineno">   74</span>&#160;</div>
<div class="line"><a name="l00075"></a><span class="lineno">   75</span>&#160;      <span class="comment">// Docu in base class</span></div>
<div class="line"><a name="l00076"></a><span class="lineno">   76</span>&#160;      <span class="keyword">virtual</span> <span class="keywordtype">void</span> endElement(<span class="keyword">const</span> XMLCh * <span class="keyword">const</span> <span class="comment">/*uri*/</span>, <span class="keyword">const</span> XMLCh * <span class="keyword">const</span> <span class="comment">/*local_name*/</span>, <span class="keyword">const</span> XMLCh * <span class="keyword">const</span> qname);</div>
<div class="line"><a name="l00077"></a><span class="lineno">   77</span>&#160;</div>
<div class="line"><a name="l00078"></a><span class="lineno">   78</span>&#160;      <span class="comment">// Docu in base class</span></div>
<div class="line"><a name="l00079"></a><span class="lineno">   79</span>&#160;      <span class="keyword">virtual</span> <span class="keywordtype">void</span> startElement(<span class="keyword">const</span> XMLCh * <span class="keyword">const</span> <span class="comment">/*uri*/</span>, <span class="keyword">const</span> XMLCh * <span class="keyword">const</span> <span class="comment">/*local_name*/</span>, <span class="keyword">const</span> XMLCh * <span class="keyword">const</span> qname, <span class="keyword">const</span> xercesc::Attributes &amp; attributes);</div>
<div class="line"><a name="l00080"></a><span class="lineno">   80</span>&#160;</div>
<div class="line"><a name="l00081"></a><span class="lineno">   81</span>&#160;      <span class="comment">// Docu in base class</span></div>
<div class="line"><a name="l00082"></a><span class="lineno">   82</span>&#160;      <span class="keyword">virtual</span> <span class="keywordtype">void</span> characters(<span class="keyword">const</span> XMLCh * <span class="keyword">const</span> chars, <span class="keyword">const</span> XMLSize_t length);</div>
<div class="line"><a name="l00083"></a><span class="lineno">   83</span>&#160;</div>
<div class="line"><a name="l00084"></a><span class="lineno">   84</span>&#160;      <span class="comment">//Docu in base class</span></div>
<div class="line"><a name="l00085"></a><span class="lineno">   85</span>&#160;      <span class="keyword">virtual</span> <span class="keywordtype">void</span> writeTo(std::ostream &amp; os);</div>
<div class="line"><a name="l00086"></a><span class="lineno">   86</span>&#160;</div>
<div class="line"><a name="l00087"></a><span class="lineno">   87</span>&#160;<span class="keyword">protected</span>:</div>
<div class="line"><a name="l00088"></a><span class="lineno">   88</span>&#160;</div>
<div class="line"><a name="l00090"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1TraMLHandler.html#a4e6e1cb4f8a8a0c70887c3568b86348e">   90</a></span>&#160;      <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a> &amp; <a class="code" href="classOpenMS_1_1Internal_1_1TraMLHandler.html#a4e6e1cb4f8a8a0c70887c3568b86348e">logger_</a>;</div>
<div class="line"><a name="l00091"></a><span class="lineno">   91</span>&#160;</div>
<div class="line"><a name="l00093"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1TraMLHandler.html#a4e6fb8ab8655403a2cb4f07d72559cd7">   93</a></span>&#160;      <a class="code" href="classOpenMS_1_1ControlledVocabulary.html">ControlledVocabulary</a> <a class="code" href="classOpenMS_1_1Internal_1_1TraMLHandler.html#a4e6fb8ab8655403a2cb4f07d72559cd7">cv_</a>;</div>
<div class="line"><a name="l00094"></a><span class="lineno">   94</span>&#160;</div>
<div class="line"><a name="l00095"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1TraMLHandler.html#a4efa4aca7642864fed4e7e4cca9e2a79">   95</a></span>&#160;      <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1Internal_1_1TraMLHandler.html#a4efa4aca7642864fed4e7e4cca9e2a79">tag_</a>;</div>
<div class="line"><a name="l00096"></a><span class="lineno">   96</span>&#160;</div>
<div class="line"><a name="l00097"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1TraMLHandler.html#a62a9584719226d386d487f8fd1b6c148">   97</a></span>&#160;      <a class="code" href="classOpenMS_1_1TargetedExperiment.html">TargetedExperiment</a> * <a class="code" href="classOpenMS_1_1Internal_1_1TraMLHandler.html#a62a9584719226d386d487f8fd1b6c148">exp_</a>;</div>
<div class="line"><a name="l00098"></a><span class="lineno">   98</span>&#160;</div>
<div class="line"><a name="l00099"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1TraMLHandler.html#a358abfca36c021378df7cdb7ad008aa0">   99</a></span>&#160;      <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1TargetedExperiment.html">TargetedExperiment</a> * <a class="code" href="classOpenMS_1_1Internal_1_1TraMLHandler.html#a358abfca36c021378df7cdb7ad008aa0">cexp_</a>;</div>
<div class="line"><a name="l00100"></a><span class="lineno">  100</span>&#160;</div>
<div class="line"><a name="l00101"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1TraMLHandler.html#a56e254e778dfc73fe999fee0644aa9f3">  101</a></span>&#160;      <a class="code" href="structOpenMS_1_1TargetedExperimentHelper_1_1Publication.html">TargetedExperiment::Publication</a> <a class="code" href="classOpenMS_1_1Internal_1_1TraMLHandler.html#a56e254e778dfc73fe999fee0644aa9f3">actual_publication_</a>;</div>
<div class="line"><a name="l00102"></a><span class="lineno">  102</span>&#160;</div>
<div class="line"><a name="l00103"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1TraMLHandler.html#a53a859cad14220e21cfca51751038495">  103</a></span>&#160;      <a class="code" href="structOpenMS_1_1TargetedExperimentHelper_1_1Contact.html">TargetedExperiment::Contact</a> <a class="code" href="classOpenMS_1_1Internal_1_1TraMLHandler.html#a53a859cad14220e21cfca51751038495">actual_contact_</a>;</div>
<div class="line"><a name="l00104"></a><span class="lineno">  104</span>&#160;</div>
<div class="line"><a name="l00105"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1TraMLHandler.html#ac3e740252c73f3ac628d50daeef6e2da">  105</a></span>&#160;      <a class="code" href="structOpenMS_1_1TargetedExperimentHelper_1_1Instrument.html">TargetedExperiment::Instrument</a> <a class="code" href="classOpenMS_1_1Internal_1_1TraMLHandler.html#ac3e740252c73f3ac628d50daeef6e2da">actual_instrument_</a>;</div>
<div class="line"><a name="l00106"></a><span class="lineno">  106</span>&#160;</div>
<div class="line"><a name="l00107"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1TraMLHandler.html#ae4fd60017080711f0adbc6ea2bb5f362">  107</a></span>&#160;      <a class="code" href="structOpenMS_1_1TargetedExperimentHelper_1_1Prediction.html">TargetedExperiment::Prediction</a> <a class="code" href="classOpenMS_1_1Internal_1_1TraMLHandler.html#ae4fd60017080711f0adbc6ea2bb5f362">actual_prediction_</a>;</div>
<div class="line"><a name="l00108"></a><span class="lineno">  108</span>&#160;</div>
<div class="line"><a name="l00109"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1TraMLHandler.html#aecdce89cce669899eff616f8d02c80a1">  109</a></span>&#160;      <a class="code" href="classOpenMS_1_1Software.html">Software</a> <a class="code" href="classOpenMS_1_1Internal_1_1TraMLHandler.html#aecdce89cce669899eff616f8d02c80a1">actual_software_</a>;</div>
<div class="line"><a name="l00110"></a><span class="lineno">  110</span>&#160;</div>
<div class="line"><a name="l00111"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1TraMLHandler.html#aef104b4639d3f1625210fe2033662dbe">  111</a></span>&#160;      <a class="code" href="structOpenMS_1_1TargetedExperimentHelper_1_1Protein.html">TargetedExperiment::Protein</a> <a class="code" href="classOpenMS_1_1Internal_1_1TraMLHandler.html#aef104b4639d3f1625210fe2033662dbe">actual_protein_</a>;</div>
<div class="line"><a name="l00112"></a><span class="lineno">  112</span>&#160;</div>
<div class="line"><a name="l00113"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1TraMLHandler.html#a2aa4980ce934f6428f7ca730de8a2b2c">  113</a></span>&#160;      <a class="code" href="classOpenMS_1_1TargetedExperimentHelper_1_1RetentionTime.html">TargetedExperiment::RetentionTime</a> <a class="code" href="classOpenMS_1_1Internal_1_1TraMLHandler.html#a2aa4980ce934f6428f7ca730de8a2b2c">actual_rt_</a>;</div>
<div class="line"><a name="l00114"></a><span class="lineno">  114</span>&#160;</div>
<div class="line"><a name="l00115"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1TraMLHandler.html#a1e30bfe3486ea0d7dd095d04448edcca">  115</a></span>&#160;      <a class="code" href="classOpenMS_1_1TargetedExperimentHelper_1_1Peptide.html">TargetedExperiment::Peptide</a> <a class="code" href="classOpenMS_1_1Internal_1_1TraMLHandler.html#a1e30bfe3486ea0d7dd095d04448edcca">actual_peptide_</a>;</div>
<div class="line"><a name="l00116"></a><span class="lineno">  116</span>&#160;</div>
<div class="line"><a name="l00117"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1TraMLHandler.html#aa2c582ba7ae294b2760b13f3f76528e4">  117</a></span>&#160;      <a class="code" href="classOpenMS_1_1TargetedExperimentHelper_1_1Compound.html">TargetedExperiment::Compound</a> <a class="code" href="classOpenMS_1_1Internal_1_1TraMLHandler.html#aa2c582ba7ae294b2760b13f3f76528e4">actual_compound_</a>;</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"><a class="line" href="classOpenMS_1_1Internal_1_1TraMLHandler.html#a2366f28ba27d6fd4b5488c8ad4461318">  119</a></span>&#160;      <a class="code" href="classOpenMS_1_1ReactionMonitoringTransition.html">ReactionMonitoringTransition</a> <a class="code" href="classOpenMS_1_1Internal_1_1TraMLHandler.html#a2366f28ba27d6fd4b5488c8ad4461318">actual_transition_</a>;</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"><a class="line" href="classOpenMS_1_1Internal_1_1TraMLHandler.html#aef70be2e392164c3336eba95987fc5b6">  121</a></span>&#160;      <a class="code" href="classOpenMS_1_1IncludeExcludeTarget.html">IncludeExcludeTarget</a> <a class="code" href="classOpenMS_1_1Internal_1_1TraMLHandler.html#aef70be2e392164c3336eba95987fc5b6">actual_target_</a>;</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"><a class="line" href="classOpenMS_1_1Internal_1_1TraMLHandler.html#a520c90f4749c4d3b5b1b149b763b5bff">  123</a></span>&#160;      <a class="code" href="classOpenMS_1_1CVTermList.html">CVTermList</a> <a class="code" href="classOpenMS_1_1Internal_1_1TraMLHandler.html#a520c90f4749c4d3b5b1b149b763b5bff">actual_validation_</a>;</div>
<div class="line"><a name="l00124"></a><span class="lineno">  124</span>&#160;</div>
<div class="line"><a name="l00125"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1TraMLHandler.html#a328a0477d358bc7588547bff41d9e051">  125</a></span>&#160;      <a class="code" href="classOpenMS_1_1CVTermList.html">CVTermList</a> <a class="code" href="classOpenMS_1_1Internal_1_1TraMLHandler.html#a328a0477d358bc7588547bff41d9e051">actual_interpretation_</a>;</div>
<div class="line"><a name="l00126"></a><span class="lineno">  126</span>&#160;</div>
<div class="line"><a name="l00127"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1TraMLHandler.html#a0eeb1544d7edd7ec6866f6c7ea5a2022">  127</a></span>&#160;      std::vector&lt;ReactionMonitoringTransition::Product&gt; <a class="code" href="classOpenMS_1_1Internal_1_1TraMLHandler.html#a0eeb1544d7edd7ec6866f6c7ea5a2022">actual_intermediate_products_</a>;</div>
<div class="line"><a name="l00128"></a><span class="lineno">  128</span>&#160;</div>
<div class="line"><a name="l00129"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1TraMLHandler.html#a05279c5b44523f8ed4006b803eb2d343">  129</a></span>&#160;      <a class="code" href="structOpenMS_1_1TargetedExperimentHelper_1_1TraMLProduct.html">ReactionMonitoringTransition::Product</a> <a class="code" href="classOpenMS_1_1Internal_1_1TraMLHandler.html#a05279c5b44523f8ed4006b803eb2d343">actual_product_</a>;</div>
<div class="line"><a name="l00130"></a><span class="lineno">  130</span>&#160;</div>
<div class="line"><a name="l00131"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1TraMLHandler.html#a60d569b204b71859ef4a09f5f641ec6e">  131</a></span>&#160;      <a class="code" href="structOpenMS_1_1TargetedExperimentHelper_1_1Configuration.html">ReactionMonitoringTransition::Configuration</a> <a class="code" href="classOpenMS_1_1Internal_1_1TraMLHandler.html#a60d569b204b71859ef4a09f5f641ec6e">actual_configuration_</a>;</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"><a class="line" href="classOpenMS_1_1Internal_1_1TraMLHandler.html#a5bcb80481988520ad0e87c8002dc771b">  133</a></span>&#160;      <a class="code" href="classOpenMS_1_1SourceFile.html">SourceFile</a> <a class="code" href="classOpenMS_1_1Internal_1_1TraMLHandler.html#a5bcb80481988520ad0e87c8002dc771b">actual_sourcefile_</a>;</div>
<div class="line"><a name="l00134"></a><span class="lineno">  134</span>&#160;</div>
<div class="line"><a name="l00136"></a><span class="lineno">  136</span>&#160;      <span class="keywordtype">void</span> handleCVParam_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; parent_parent_tag, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; parent_tag, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1CVTerm.html">CVTerm</a> &amp; cv_term);</div>
<div class="line"><a name="l00137"></a><span class="lineno">  137</span>&#160;</div>
<div class="line"><a name="l00139"></a><span class="lineno">  139</span>&#160;      <span class="keywordtype">void</span> handleUserParam_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; parent_parent_tag, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; parent_tag, <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_1String.html">String</a> &amp; type, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; value);</div>
<div class="line"><a name="l00140"></a><span class="lineno">  140</span>&#160;</div>
<div class="line"><a name="l00142"></a><span class="lineno">  142</span>&#160;      <span class="keywordtype">void</span> writeUserParam_(std::ostream &amp; os, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MetaInfoInterface.html">MetaInfoInterface</a> &amp; meta, <a class="code" href="classunsigned_01int.html">UInt</a> indent) <span class="keyword">const</span>;</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> writeUserParams_(std::ostream &amp; os, <span class="keyword">const</span> std::vector&lt;MetaInfoInterface&gt; &amp; meta, <a class="code" href="classunsigned_01int.html">UInt</a> indent) <span class="keyword">const</span>;</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="keywordtype">void</span> writeCVParams_(std::ostream &amp; os, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1CVTermList.html">CVTermList</a> &amp; cv_terms, <a class="code" href="classunsigned_01int.html">UInt</a> indent) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00147"></a><span class="lineno">  147</span>&#160;</div>
<div class="line"><a name="l00148"></a><span class="lineno">  148</span>&#160;      <span class="comment">// subfunctions of write</span></div>
<div class="line"><a name="l00149"></a><span class="lineno">  149</span>&#160;      <span class="keywordtype">void</span> writeTarget_(std::ostream &amp; os, <span class="keyword">const</span> std::vector&lt;IncludeExcludeTarget&gt;::const_iterator &amp; it) <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> writeProduct_(std::ostream &amp; os, <span class="keyword">const</span> std::vector&lt;ReactionMonitoringTransition::Product&gt;::const_iterator &amp; prod_it) <span class="keyword">const</span>;</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="keywordtype">void</span> writeConfiguration_(std::ostream &amp; os, <span class="keyword">const</span> std::vector&lt;ReactionMonitoringTransition::Configuration&gt;::const_iterator &amp; cit) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00154"></a><span class="lineno">  154</span>&#160;</div>
<div class="line"><a name="l00156"></a><span class="lineno">  156</span>&#160;      <a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html">ControlledVocabulary::CVTerm</a> getChildWithName_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; parent_accession, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; name) <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="l00159"></a><span class="lineno">  159</span>&#160;      <span class="comment">//void writeSourceFile_(std::ostream&amp; os, const String&amp; id, const SourceFile&amp; software);</span></div>
<div class="line"><a name="l00160"></a><span class="lineno">  160</span>&#160;</div>
<div class="line"><a name="l00161"></a><span class="lineno">  161</span>&#160;<span class="keyword">private</span>:</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;      <a class="code" href="classOpenMS_1_1Internal_1_1TraMLHandler.html">TraMLHandler</a>();</div>
<div class="line"><a name="l00164"></a><span class="lineno">  164</span>&#160;      <a class="code" href="classOpenMS_1_1Internal_1_1TraMLHandler.html">TraMLHandler</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1Internal_1_1TraMLHandler.html">TraMLHandler</a> &amp; rhs);</div>
<div class="line"><a name="l00165"></a><span class="lineno">  165</span>&#160;      <a class="code" href="classOpenMS_1_1Internal_1_1TraMLHandler.html">TraMLHandler</a> &amp; operator=(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1Internal_1_1TraMLHandler.html">TraMLHandler</a> &amp; rhs);</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="comment">// namespace Internal</span></div>
<div class="line"><a name="l00168"></a><span class="lineno">  168</span>&#160;} <span class="comment">// namespace OpenMS</span></div>
<div class="line"><a name="l00169"></a><span class="lineno">  169</span>&#160;</div>
<div class="line"><a name="l00170"></a><span class="lineno">  170</span>&#160;<span class="preprocessor">#endif</span></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1TraMLHandler_html_ae4fd60017080711f0adbc6ea2bb5f362"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1TraMLHandler.html#ae4fd60017080711f0adbc6ea2bb5f362">OpenMS::Internal::TraMLHandler::actual_prediction_</a></div><div class="ttdeci">TargetedExperiment::Prediction actual_prediction_</div><div class="ttdef"><b>Definition:</b> TraMLHandler.h:107</div></div>
<div class="ttc" id="classunsigned_01int_html"><div class="ttname"><a href="classunsigned_01int.html">unsigned int</a></div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1TraMLHandler_html_a1e30bfe3486ea0d7dd095d04448edcca"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1TraMLHandler.html#a1e30bfe3486ea0d7dd095d04448edcca">OpenMS::Internal::TraMLHandler::actual_peptide_</a></div><div class="ttdeci">TargetedExperiment::Peptide actual_peptide_</div><div class="ttdef"><b>Definition:</b> TraMLHandler.h:115</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="structOpenMS_1_1ControlledVocabulary_1_1CVTerm_html"><div class="ttname"><a href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html">OpenMS::ControlledVocabulary::CVTerm</a></div><div class="ttdoc">Representation of a CV term. </div><div class="ttdef"><b>Definition:</b> ControlledVocabulary.h:60</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_1Internal_1_1TraMLHandler_html_aef104b4639d3f1625210fe2033662dbe"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1TraMLHandler.html#aef104b4639d3f1625210fe2033662dbe">OpenMS::Internal::TraMLHandler::actual_protein_</a></div><div class="ttdeci">TargetedExperiment::Protein actual_protein_</div><div class="ttdef"><b>Definition:</b> TraMLHandler.h:111</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1TraMLHandler_html_a4efa4aca7642864fed4e7e4cca9e2a79"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1TraMLHandler.html#a4efa4aca7642864fed4e7e4cca9e2a79">OpenMS::Internal::TraMLHandler::tag_</a></div><div class="ttdeci">String tag_</div><div class="ttdef"><b>Definition:</b> TraMLHandler.h:95</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="classOpenMS_1_1Internal_1_1TraMLHandler_html_aecdce89cce669899eff616f8d02c80a1"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1TraMLHandler.html#aecdce89cce669899eff616f8d02c80a1">OpenMS::Internal::TraMLHandler::actual_software_</a></div><div class="ttdeci">Software actual_software_</div><div class="ttdef"><b>Definition:</b> TraMLHandler.h:109</div></div>
<div class="ttc" id="ControlledVocabulary_8h_html"><div class="ttname"><a href="ControlledVocabulary_8h.html">ControlledVocabulary.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1TraMLHandler_html_a12660f60dd5d2eb3fe66e2c819199465"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1TraMLHandler.html#a12660f60dd5d2eb3fe66e2c819199465">OpenMS::Internal::TraMLHandler::ConfigurationListType</a></div><div class="ttdeci">std::vector&lt; ReactionMonitoringTransition::Configuration &gt; ConfigurationListType</div><div class="ttdef"><b>Definition:</b> TraMLHandler.h:60</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_1Internal_1_1TraMLHandler_html_a328a0477d358bc7588547bff41d9e051"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1TraMLHandler.html#a328a0477d358bc7588547bff41d9e051">OpenMS::Internal::TraMLHandler::actual_interpretation_</a></div><div class="ttdeci">CVTermList actual_interpretation_</div><div class="ttdef"><b>Definition:</b> TraMLHandler.h:125</div></div>
<div class="ttc" id="ProgressLogger_8h_html"><div class="ttname"><a href="ProgressLogger_8h.html">ProgressLogger.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1TraMLHandler_html_a2aa4980ce934f6428f7ca730de8a2b2c"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1TraMLHandler.html#a2aa4980ce934f6428f7ca730de8a2b2c">OpenMS::Internal::TraMLHandler::actual_rt_</a></div><div class="ttdeci">TargetedExperiment::RetentionTime actual_rt_</div><div class="ttdef"><b>Definition:</b> TraMLHandler.h:113</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1TraMLHandler_html"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1TraMLHandler.html">OpenMS::Internal::TraMLHandler</a></div><div class="ttdoc">XML handler for TraMLFile. </div><div class="ttdef"><b>Definition:</b> TraMLHandler.h:54</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1XMLHandler_html"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1XMLHandler.html">OpenMS::Internal::XMLHandler</a></div><div class="ttdoc">Base class for XML handlers. </div><div class="ttdef"><b>Definition:</b> XMLHandler.h:89</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="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_1Internal_1_1TraMLHandler_html_ac3e740252c73f3ac628d50daeef6e2da"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1TraMLHandler.html#ac3e740252c73f3ac628d50daeef6e2da">OpenMS::Internal::TraMLHandler::actual_instrument_</a></div><div class="ttdeci">TargetedExperiment::Instrument actual_instrument_</div><div class="ttdef"><b>Definition:</b> TraMLHandler.h:105</div></div>
<div class="ttc" id="classOpenMS_1_1ControlledVocabulary_html"><div class="ttname"><a href="classOpenMS_1_1ControlledVocabulary.html">OpenMS::ControlledVocabulary</a></div><div class="ttdoc">Representation of a controlled vocabulary. </div><div class="ttdef"><b>Definition:</b> ControlledVocabulary.h:54</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1TraMLHandler_html_a05279c5b44523f8ed4006b803eb2d343"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1TraMLHandler.html#a05279c5b44523f8ed4006b803eb2d343">OpenMS::Internal::TraMLHandler::actual_product_</a></div><div class="ttdeci">ReactionMonitoringTransition::Product actual_product_</div><div class="ttdef"><b>Definition:</b> TraMLHandler.h:129</div></div>
<div class="ttc" id="structOpenMS_1_1TargetedExperimentHelper_1_1Configuration_html"><div class="ttname"><a href="structOpenMS_1_1TargetedExperimentHelper_1_1Configuration.html">OpenMS::TargetedExperimentHelper::Configuration</a></div><div class="ttdef"><b>Definition:</b> TargetedExperimentHelper.h:55</div></div>
<div class="ttc" id="structOpenMS_1_1TargetedExperimentHelper_1_1TraMLProduct_html"><div class="ttname"><a href="structOpenMS_1_1TargetedExperimentHelper_1_1TraMLProduct.html">OpenMS::TargetedExperimentHelper::TraMLProduct</a></div><div class="ttdef"><b>Definition:</b> TargetedExperimentHelper.h:461</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1TraMLHandler_html_aa2c582ba7ae294b2760b13f3f76528e4"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1TraMLHandler.html#aa2c582ba7ae294b2760b13f3f76528e4">OpenMS::Internal::TraMLHandler::actual_compound_</a></div><div class="ttdeci">TargetedExperiment::Compound actual_compound_</div><div class="ttdef"><b>Definition:</b> TraMLHandler.h:117</div></div>
<div class="ttc" id="TargetedExperiment_8h_html"><div class="ttname"><a href="TargetedExperiment_8h.html">TargetedExperiment.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1TraMLHandler_html_aef70be2e392164c3336eba95987fc5b6"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1TraMLHandler.html#aef70be2e392164c3336eba95987fc5b6">OpenMS::Internal::TraMLHandler::actual_target_</a></div><div class="ttdeci">IncludeExcludeTarget actual_target_</div><div class="ttdef"><b>Definition:</b> TraMLHandler.h:121</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_1Internal_1_1TraMLHandler_html_a4e6e1cb4f8a8a0c70887c3568b86348e"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1TraMLHandler.html#a4e6e1cb4f8a8a0c70887c3568b86348e">OpenMS::Internal::TraMLHandler::logger_</a></div><div class="ttdeci">const ProgressLogger &amp; logger_</div><div class="ttdoc">Progress logger. </div><div class="ttdef"><b>Definition:</b> TraMLHandler.h:90</div></div>
<div class="ttc" id="classOpenMS_1_1MetaInfoInterface_html"><div class="ttname"><a href="classOpenMS_1_1MetaInfoInterface.html">OpenMS::MetaInfoInterface</a></div><div class="ttdoc">Interface for classes that can store arbitrary meta information (Type-Name-Value tuples). </div><div class="ttdef"><b>Definition:</b> MetaInfoInterface.h:61</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1TraMLHandler_html_a53a859cad14220e21cfca51751038495"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1TraMLHandler.html#a53a859cad14220e21cfca51751038495">OpenMS::Internal::TraMLHandler::actual_contact_</a></div><div class="ttdeci">TargetedExperiment::Contact actual_contact_</div><div class="ttdef"><b>Definition:</b> TraMLHandler.h:103</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_1Internal_1_1TraMLHandler_html_a4e6fb8ab8655403a2cb4f07d72559cd7"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1TraMLHandler.html#a4e6fb8ab8655403a2cb4f07d72559cd7">OpenMS::Internal::TraMLHandler::cv_</a></div><div class="ttdeci">ControlledVocabulary cv_</div><div class="ttdoc">Controlled vocabulary (psi-ms from OpenMS/share/OpenMS/CV/psi-ms.obo) </div><div class="ttdef"><b>Definition:</b> TraMLHandler.h:93</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1TraMLHandler_html_a60d569b204b71859ef4a09f5f641ec6e"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1TraMLHandler.html#a60d569b204b71859ef4a09f5f641ec6e">OpenMS::Internal::TraMLHandler::actual_configuration_</a></div><div class="ttdeci">ReactionMonitoringTransition::Configuration actual_configuration_</div><div class="ttdef"><b>Definition:</b> TraMLHandler.h:131</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_1ProgressLogger_html"><div class="ttname"><a href="classOpenMS_1_1ProgressLogger.html">OpenMS::ProgressLogger</a></div><div class="ttdoc">Base class for all classes that want to report their progess. </div><div class="ttdef"><b>Definition:</b> ProgressLogger.h:56</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="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_1Internal_1_1TraMLHandler_html_a2366f28ba27d6fd4b5488c8ad4461318"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1TraMLHandler.html#a2366f28ba27d6fd4b5488c8ad4461318">OpenMS::Internal::TraMLHandler::actual_transition_</a></div><div class="ttdeci">ReactionMonitoringTransition actual_transition_</div><div class="ttdef"><b>Definition:</b> TraMLHandler.h:119</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="classOpenMS_1_1Internal_1_1TraMLHandler_html_a56e254e778dfc73fe999fee0644aa9f3"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1TraMLHandler.html#a56e254e778dfc73fe999fee0644aa9f3">OpenMS::Internal::TraMLHandler::actual_publication_</a></div><div class="ttdeci">TargetedExperiment::Publication actual_publication_</div><div class="ttdef"><b>Definition:</b> TraMLHandler.h:101</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1TraMLHandler_html_a62a9584719226d386d487f8fd1b6c148"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1TraMLHandler.html#a62a9584719226d386d487f8fd1b6c148">OpenMS::Internal::TraMLHandler::exp_</a></div><div class="ttdeci">TargetedExperiment * exp_</div><div class="ttdef"><b>Definition:</b> TraMLHandler.h:97</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1TraMLHandler_html_a50ebcf434b59ba84992d03316e3a1628"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1TraMLHandler.html#a50ebcf434b59ba84992d03316e3a1628">OpenMS::Internal::TraMLHandler::ProductListType</a></div><div class="ttdeci">std::vector&lt; ReactionMonitoringTransition::Product &gt; ProductListType</div><div class="ttdef"><b>Definition:</b> TraMLHandler.h:59</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1TraMLHandler_html_a0eeb1544d7edd7ec6866f6c7ea5a2022"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1TraMLHandler.html#a0eeb1544d7edd7ec6866f6c7ea5a2022">OpenMS::Internal::TraMLHandler::actual_intermediate_products_</a></div><div class="ttdeci">std::vector&lt; ReactionMonitoringTransition::Product &gt; actual_intermediate_products_</div><div class="ttdef"><b>Definition:</b> TraMLHandler.h:127</div></div>
<div class="ttc" id="XMLHandler_8h_html"><div class="ttname"><a href="XMLHandler_8h.html">XMLHandler.h</a></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_1Internal_1_1TraMLHandler_html_a5bcb80481988520ad0e87c8002dc771b"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1TraMLHandler.html#a5bcb80481988520ad0e87c8002dc771b">OpenMS::Internal::TraMLHandler::actual_sourcefile_</a></div><div class="ttdeci">SourceFile actual_sourcefile_</div><div class="ttdef"><b>Definition:</b> TraMLHandler.h:133</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1TraMLHandler_html_a520c90f4749c4d3b5b1b149b763b5bff"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1TraMLHandler.html#a520c90f4749c4d3b5b1b149b763b5bff">OpenMS::Internal::TraMLHandler::actual_validation_</a></div><div class="ttdeci">CVTermList actual_validation_</div><div class="ttdef"><b>Definition:</b> TraMLHandler.h:123</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_1Internal_1_1TraMLHandler_html_a358abfca36c021378df7cdb7ad008aa0"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1TraMLHandler.html#a358abfca36c021378df7cdb7ad008aa0">OpenMS::Internal::TraMLHandler::cexp_</a></div><div class="ttdeci">const TargetedExperiment * cexp_</div><div class="ttdef"><b>Definition:</b> TraMLHandler.h:99</div></div>
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