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<a href="FeatureFinderDefs_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> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="comment">// OpenMS -- Open-Source Mass Spectrometry</span></div>
<div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <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> <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> <span class="comment">//</span></div>
<div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <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> <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> <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> <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> <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> <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> <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> <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> <span class="comment">// without specific prior written permission.</span></div>
<div class="line"><a name="l00016"></a><span class="lineno"> 16</span> <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> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00018"></a><span class="lineno"> 18</span> <span class="comment">// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"</span></div>
<div class="line"><a name="l00019"></a><span class="lineno"> 19</span> <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> <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> <span class="comment">// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING</span></div>
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<div class="line"><a name="l00027"></a><span class="lineno"> 27</span> <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> <span class="comment">// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</span></div>
<div class="line"><a name="l00029"></a><span class="lineno"> 29</span> <span class="comment">//</span></div>
<div class="line"><a name="l00030"></a><span class="lineno"> 30</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00031"></a><span class="lineno"> 31</span> <span class="comment">// $Maintainer: Clemens Groepl $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno"> 32</span> <span class="comment">// $Authors: $</span></div>
<div class="line"><a name="l00033"></a><span class="lineno"> 33</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00034"></a><span class="lineno"> 34</span> </div>
<div class="line"><a name="l00035"></a><span class="lineno"> 35</span> <span class="preprocessor">#ifndef OPENMS_TRANSFORMATIONS_FEATUREFINDER_FEATUREFINDERDEFS_H</span></div>
<div class="line"><a name="l00036"></a><span class="lineno"> 36</span> <span class="preprocessor"></span><span class="preprocessor">#define OPENMS_TRANSFORMATIONS_FEATUREFINDER_FEATUREFINDERDEFS_H</span></div>
<div class="line"><a name="l00037"></a><span class="lineno"> 37</span> <span class="preprocessor"></span></div>
<div class="line"><a name="l00038"></a><span class="lineno"> 38</span> </div>
<div class="line"><a name="l00039"></a><span class="lineno"> 39</span> <span class="preprocessor">#include <<a class="code" href="IsotopeCluster_8h.html">OpenMS/DATASTRUCTURES/IsotopeCluster.h</a>></span></div>
<div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="preprocessor">#include <<a class="code" href="String_8h.html">OpenMS/DATASTRUCTURES/String.h</a>></span></div>
<div class="line"><a name="l00041"></a><span class="lineno"> 41</span> <span class="preprocessor">#include <<a class="code" href="Exception_8h.html">OpenMS/CONCEPT/Exception.h</a>></span></div>
<div class="line"><a name="l00042"></a><span class="lineno"> 42</span> <span class="preprocessor">#include <<a class="code" href="GlobalExceptionHandler_8h.html">OpenMS/CONCEPT/GlobalExceptionHandler.h</a>></span></div>
<div class="line"><a name="l00043"></a><span class="lineno"> 43</span> </div>
<div class="line"><a name="l00044"></a><span class="lineno"> 44</span> <span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00045"></a><span class="lineno"> 45</span> {</div>
<div class="line"><a name="l00046"></a><span class="lineno"> 46</span> </div>
<div class="line"><a name="l00047"></a><span class="lineno"> 47</span>  <span class="comment">// forward declaration</span></div>
<div class="line"><a name="l00048"></a><span class="lineno"> 48</span>  <span class="keyword">class </span>FeatureFinder;</div>
<div class="line"><a name="l00049"></a><span class="lineno"> 49</span> </div>
<div class="line"><a name="l00051"></a><span class="lineno"><a class="line" href="structOpenMS_1_1FeatureFinderDefs.html"> 51</a></span>  <span class="keyword">struct </span>OPENMS_DLLAPI <a class="code" href="structOpenMS_1_1FeatureFinderDefs.html">FeatureFinderDefs</a></div>
<div class="line"><a name="l00052"></a><span class="lineno"> 52</span>  {</div>
<div class="line"><a name="l00054"></a><span class="lineno"><a class="line" href="structOpenMS_1_1FeatureFinderDefs.html#aaee0bfd850887fdc58115cead9e9b8b9"> 54</a></span>  <span class="keyword">typedef</span> <a class="code" href="structOpenMS_1_1IsotopeCluster.html#a0cab124671a3ada269f0553e1c8934da">IsotopeCluster::IndexPair</a> <a class="code" href="structOpenMS_1_1FeatureFinderDefs.html#aaee0bfd850887fdc58115cead9e9b8b9">IndexPair</a>;</div>
<div class="line"><a name="l00055"></a><span class="lineno"> 55</span> </div>
<div class="line"><a name="l00057"></a><span class="lineno"><a class="line" href="structOpenMS_1_1FeatureFinderDefs.html#af01a99958d0b18999737158daf8820ac"> 57</a></span>  <span class="keyword">typedef</span> <a class="code" href="structOpenMS_1_1IsotopeCluster_1_1ChargedIndexSet.html">IsotopeCluster::ChargedIndexSet</a> <a class="code" href="structOpenMS_1_1FeatureFinderDefs.html#af01a99958d0b18999737158daf8820ac">ChargedIndexSet</a>;</div>
<div class="line"><a name="l00058"></a><span class="lineno"> 58</span> </div>
<div class="line"><a name="l00060"></a><span class="lineno"><a class="line" href="structOpenMS_1_1FeatureFinderDefs.html#af7439235b89a75354a2e87350e36834f"> 60</a></span>  <span class="keyword">typedef</span> <a class="code" href="structOpenMS_1_1IsotopeCluster.html#aed4049efd4228c847ab300ac4c466eca">IsotopeCluster::IndexSet</a> <a class="code" href="structOpenMS_1_1FeatureFinderDefs.html#af7439235b89a75354a2e87350e36834f">IndexSet</a>;</div>
<div class="line"><a name="l00061"></a><span class="lineno"> 61</span> </div>
<div class="line"><a name="l00063"></a><span class="lineno"><a class="line" href="structOpenMS_1_1FeatureFinderDefs.html#a3f3de3e0d751949b8d0b60ffb302944aa1e780c62cb3fd2edcac39f739bbe6f6c"> 63</a></span>  <span class="keyword">enum</span> <a class="code" href="structOpenMS_1_1FeatureFinderDefs.html#a3f3de3e0d751949b8d0b60ffb302944a">Flag</a> {UNUSED, USED};</div>
<div class="line"><a name="l00064"></a><span class="lineno"> 64</span> </div>
<div class="line"><a name="l00066"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderDefs_1_1NoSuccessor.html"> 66</a></span>  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1FeatureFinderDefs_1_1NoSuccessor.html">NoSuccessor</a> :</div>
<div class="line"><a name="l00067"></a><span class="lineno"> 67</span>  <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1Exception_1_1BaseException.html">Exception::BaseException</a></div>
<div class="line"><a name="l00068"></a><span class="lineno"> 68</span>  {</div>
<div class="line"><a name="l00069"></a><span class="lineno"> 69</span> <span class="keyword">public</span>:</div>
<div class="line"><a name="l00070"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderDefs_1_1NoSuccessor.html#a7baccfea38c14cbd016c19b07cf82ad9"> 70</a></span>  <a class="code" href="classOpenMS_1_1FeatureFinderDefs_1_1NoSuccessor.html#a7baccfea38c14cbd016c19b07cf82ad9">NoSuccessor</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> * file, <span class="keywordtype">int</span> line, <span class="keyword">const</span> <span class="keywordtype">char</span> * <span class="keyword">function</span>, <span class="keyword">const</span> <a class="code" href="structOpenMS_1_1FeatureFinderDefs.html#aaee0bfd850887fdc58115cead9e9b8b9">IndexPair</a> & index) :</div>
<div class="line"><a name="l00071"></a><span class="lineno"> 71</span>  BaseException(file, line, function, <span class="stringliteral">"NoSuccessor"</span>, <span class="stringliteral">"no successor/predecessor"</span>),</div>
<div class="line"><a name="l00072"></a><span class="lineno"> 72</span>  index_(index)</div>
<div class="line"><a name="l00073"></a><span class="lineno"> 73</span>  {</div>
<div class="line"><a name="l00074"></a><span class="lineno"> 74</span>  what_ = <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">"there is no successor/predecessor for the given Index: "</span>) + index_.first + <span class="stringliteral">"/"</span> + index_.second;</div>
<div class="line"><a name="l00075"></a><span class="lineno"> 75</span>  <a class="code" href="classOpenMS_1_1Exception_1_1GlobalExceptionHandler.html#a0f5c900ab953d53026d2aa977cfc6ace">Exception::GlobalExceptionHandler::getInstance</a>().<a class="code" href="classOpenMS_1_1Exception_1_1GlobalExceptionHandler.html#ac351f48d2668c8df16d673b044ff997c">setMessage</a>(what_);</div>
<div class="line"><a name="l00076"></a><span class="lineno"> 76</span>  }</div>
<div class="line"><a name="l00077"></a><span class="lineno"> 77</span> </div>
<div class="line"><a name="l00078"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderDefs_1_1NoSuccessor.html#a205d14b3e5c5c57b350bc5f06813db21"> 78</a></span>  <span class="keyword">virtual</span> <a class="code" href="classOpenMS_1_1FeatureFinderDefs_1_1NoSuccessor.html#a205d14b3e5c5c57b350bc5f06813db21">~NoSuccessor</a>() throw()</div>
<div class="line"><a name="l00079"></a><span class="lineno"> 79</span>  {</div>
<div class="line"><a name="l00080"></a><span class="lineno"> 80</span>  }</div>
<div class="line"><a name="l00081"></a><span class="lineno"> 81</span> </div>
<div class="line"><a name="l00082"></a><span class="lineno"> 82</span> <span class="keyword">protected</span>:</div>
<div class="line"><a name="l00083"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderDefs_1_1NoSuccessor.html#acc57fd6ab902886ca0e47bfc2dc76ccb"> 83</a></span>  <a class="code" href="structOpenMS_1_1FeatureFinderDefs.html#aaee0bfd850887fdc58115cead9e9b8b9">IndexPair</a> <a class="code" href="classOpenMS_1_1FeatureFinderDefs_1_1NoSuccessor.html#acc57fd6ab902886ca0e47bfc2dc76ccb">index_</a>; <span class="comment">// index without successor/predecessor</span></div>
<div class="line"><a name="l00084"></a><span class="lineno"> 84</span>  };</div>
<div class="line"><a name="l00085"></a><span class="lineno"> 85</span>  };</div>
<div class="line"><a name="l00086"></a><span class="lineno"> 86</span> }</div>
<div class="line"><a name="l00087"></a><span class="lineno"> 87</span> <span class="preprocessor">#endif // OPENMS_TRANSFORMATIONS_FEATUREFINDER_FEATUREFINDERDEFS_H</span></div>
<div class="ttc" id="structOpenMS_1_1FeatureFinderDefs_html_aaee0bfd850887fdc58115cead9e9b8b9"><div class="ttname"><a href="structOpenMS_1_1FeatureFinderDefs.html#aaee0bfd850887fdc58115cead9e9b8b9">OpenMS::FeatureFinderDefs::IndexPair</a></div><div class="ttdeci">IsotopeCluster::IndexPair IndexPair</div><div class="ttdoc">Index to peak consisting of two UInts (scan index / peak index) </div><div class="ttdef"><b>Definition:</b> FeatureFinderDefs.h:54</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="structOpenMS_1_1IsotopeCluster_html_a0cab124671a3ada269f0553e1c8934da"><div class="ttname"><a href="structOpenMS_1_1IsotopeCluster.html#a0cab124671a3ada269f0553e1c8934da">OpenMS::IsotopeCluster::IndexPair</a></div><div class="ttdeci">std::pair< Size, Size > IndexPair</div><div class="ttdoc">An index e.g. in an MSExperiment. </div><div class="ttdef"><b>Definition:</b> IsotopeCluster.h:48</div></div>
<div class="ttc" id="structOpenMS_1_1FeatureFinderDefs_html_a3f3de3e0d751949b8d0b60ffb302944a"><div class="ttname"><a href="structOpenMS_1_1FeatureFinderDefs.html#a3f3de3e0d751949b8d0b60ffb302944a">OpenMS::FeatureFinderDefs::Flag</a></div><div class="ttdeci">Flag</div><div class="ttdoc">Flags that indicate if a peak is already used in a feature. </div><div class="ttdef"><b>Definition:</b> FeatureFinderDefs.h:63</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderDefs_1_1NoSuccessor_html_acc57fd6ab902886ca0e47bfc2dc76ccb"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderDefs_1_1NoSuccessor.html#acc57fd6ab902886ca0e47bfc2dc76ccb">OpenMS::FeatureFinderDefs::NoSuccessor::index_</a></div><div class="ttdeci">IndexPair index_</div><div class="ttdef"><b>Definition:</b> FeatureFinderDefs.h:83</div></div>
<div class="ttc" id="structOpenMS_1_1FeatureFinderDefs_html"><div class="ttname"><a href="structOpenMS_1_1FeatureFinderDefs.html">OpenMS::FeatureFinderDefs</a></div><div class="ttdoc">The purpose of this struct is to provide definitions of classes and typedefs which are used throughou...</div><div class="ttdef"><b>Definition:</b> FeatureFinderDefs.h:51</div></div>
<div class="ttc" id="classOpenMS_1_1Exception_1_1GlobalExceptionHandler_html_a0f5c900ab953d53026d2aa977cfc6ace"><div class="ttname"><a href="classOpenMS_1_1Exception_1_1GlobalExceptionHandler.html#a0f5c900ab953d53026d2aa977cfc6ace">OpenMS::Exception::GlobalExceptionHandler::getInstance</a></div><div class="ttdeci">static GlobalExceptionHandler & getInstance()</div><div class="ttdoc">The accessor for the singleton. It also serves as a replacement for the constructor. </div><div class="ttdef"><b>Definition:</b> GlobalExceptionHandler.h:89</div></div>
<div class="ttc" id="GlobalExceptionHandler_8h_html"><div class="ttname"><a href="GlobalExceptionHandler_8h.html">GlobalExceptionHandler.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderDefs_1_1NoSuccessor_html_a7baccfea38c14cbd016c19b07cf82ad9"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderDefs_1_1NoSuccessor.html#a7baccfea38c14cbd016c19b07cf82ad9">OpenMS::FeatureFinderDefs::NoSuccessor::NoSuccessor</a></div><div class="ttdeci">NoSuccessor(const char *file, int line, const char *function, const IndexPair &index)</div><div class="ttdef"><b>Definition:</b> FeatureFinderDefs.h:70</div></div>
<div class="ttc" id="structOpenMS_1_1FeatureFinderDefs_html_af7439235b89a75354a2e87350e36834f"><div class="ttname"><a href="structOpenMS_1_1FeatureFinderDefs.html#af7439235b89a75354a2e87350e36834f">OpenMS::FeatureFinderDefs::IndexSet</a></div><div class="ttdeci">IsotopeCluster::IndexSet IndexSet</div><div class="ttdoc">A set of peak indices. </div><div class="ttdef"><b>Definition:</b> FeatureFinderDefs.h:60</div></div>
<div class="ttc" id="IsotopeCluster_8h_html"><div class="ttname"><a href="IsotopeCluster_8h.html">IsotopeCluster.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderDefs_1_1NoSuccessor_html_a205d14b3e5c5c57b350bc5f06813db21"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderDefs_1_1NoSuccessor.html#a205d14b3e5c5c57b350bc5f06813db21">OpenMS::FeatureFinderDefs::NoSuccessor::~NoSuccessor</a></div><div class="ttdeci">virtual ~NoSuccessor()</div><div class="ttdef"><b>Definition:</b> FeatureFinderDefs.h:78</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderDefs_1_1NoSuccessor_html"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderDefs_1_1NoSuccessor.html">OpenMS::FeatureFinderDefs::NoSuccessor</a></div><div class="ttdoc">Exception that is thrown if a method an invalid IndexPair is given. </div><div class="ttdef"><b>Definition:</b> FeatureFinderDefs.h:66</div></div>
<div class="ttc" id="classOpenMS_1_1Exception_1_1BaseException_html"><div class="ttname"><a href="classOpenMS_1_1Exception_1_1BaseException.html">OpenMS::Exception::BaseException</a></div><div class="ttdoc">Exception base class. </div><div class="ttdef"><b>Definition:</b> Exception.h:90</div></div>
<div class="ttc" id="structOpenMS_1_1FeatureFinderDefs_html_af01a99958d0b18999737158daf8820ac"><div class="ttname"><a href="structOpenMS_1_1FeatureFinderDefs.html#af01a99958d0b18999737158daf8820ac">OpenMS::FeatureFinderDefs::ChargedIndexSet</a></div><div class="ttdeci">IsotopeCluster::ChargedIndexSet ChargedIndexSet</div><div class="ttdoc">Index to peak consisting of two UInts (scan index / peak index) with charge information. </div><div class="ttdef"><b>Definition:</b> FeatureFinderDefs.h:57</div></div>
<div class="ttc" id="classOpenMS_1_1Exception_1_1GlobalExceptionHandler_html_ac351f48d2668c8df16d673b044ff997c"><div class="ttname"><a href="classOpenMS_1_1Exception_1_1GlobalExceptionHandler.html#ac351f48d2668c8df16d673b044ff997c">OpenMS::Exception::GlobalExceptionHandler::setMessage</a></div><div class="ttdeci">static void setMessage(const std::string &message)</div></div>
<div class="ttc" id="structOpenMS_1_1IsotopeCluster_1_1ChargedIndexSet_html"><div class="ttname"><a href="structOpenMS_1_1IsotopeCluster_1_1ChargedIndexSet.html">OpenMS::IsotopeCluster::ChargedIndexSet</a></div><div class="ttdoc">index set with associated charge estimate </div><div class="ttdef"><b>Definition:</b> IsotopeCluster.h:53</div></div>
<div class="ttc" id="structOpenMS_1_1IsotopeCluster_html_aed4049efd4228c847ab300ac4c466eca"><div class="ttname"><a href="structOpenMS_1_1IsotopeCluster.html#aed4049efd4228c847ab300ac4c466eca">OpenMS::IsotopeCluster::IndexSet</a></div><div class="ttdeci">std::set< IndexPair > IndexSet</div><div class="ttdoc">A set of index pairs, usually referring to an MSExperiment. </div><div class="ttdef"><b>Definition:</b> IsotopeCluster.h:50</div></div>
<div class="ttc" id="Exception_8h_html"><div class="ttname"><a href="Exception_8h.html">Exception.h</a></div></div>
<div class="ttc" id="String_8h_html"><div class="ttname"><a href="String_8h.html">String.h</a></div></div>
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<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:13 using doxygen 1.8.5</font></TD>
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