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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_9f700962877a340cb515a8f4e78fa50c.html">TRANSFORMATIONS</a></li><li class="navelem"><a class="el" href="dir_37e9c1b52d0b253b62f883ccdf65930c.html">FEATUREFINDER</a></li><li class="navelem"><a class="el" href="dir_85426f95c54d3036067585334ac23a8c.html">SUPERHIRN</a></li> </ul>
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<div class="title">LCElutionPeak.h</div> </div>
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27
<a href="LCElutionPeak_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>
28
<div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="comment">// OpenMS -- Open-Source Mass Spectrometry</span></div>
29
<div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
30
<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>
31
<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>
32
<div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="comment">//</span></div>
33
<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>
34
<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>
35
<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>
36
<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>
37
<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>
38
<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>
39
<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>
40
<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>
41
<div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="comment">// without specific prior written permission.</span></div>
42
<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>
43
<div class="line"><a name="l00017"></a><span class="lineno"> 17</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
44
<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>
45
<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>
46
<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>
47
<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>
48
<div class="line"><a name="l00022"></a><span class="lineno"> 22</span> <span class="comment">// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,</span></div>
49
<div class="line"><a name="l00023"></a><span class="lineno"> 23</span> <span class="comment">// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,</span></div>
50
<div class="line"><a name="l00024"></a><span class="lineno"> 24</span> <span class="comment">// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;</span></div>
51
<div class="line"><a name="l00025"></a><span class="lineno"> 25</span> <span class="comment">// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,</span></div>
52
<div class="line"><a name="l00026"></a><span class="lineno"> 26</span> <span class="comment">// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR</span></div>
53
<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>
54
<div class="line"><a name="l00028"></a><span class="lineno"> 28</span> <span class="comment">// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</span></div>
55
<div class="line"><a name="l00029"></a><span class="lineno"> 29</span> <span class="comment">//</span></div>
56
<div class="line"><a name="l00030"></a><span class="lineno"> 30</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
57
<div class="line"><a name="l00031"></a><span class="lineno"> 31</span> <span class="comment">// $Maintainer: Florian Zeller $</span></div>
58
<div class="line"><a name="l00032"></a><span class="lineno"> 32</span> <span class="comment">// $Authors: Lukas Mueller, Markus Mueller $</span></div>
59
<div class="line"><a name="l00033"></a><span class="lineno"> 33</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
60
<div class="line"><a name="l00034"></a><span class="lineno"> 34</span> <span class="comment">//</span></div>
61
<div class="line"><a name="l00036"></a><span class="lineno"> 36</span> <span class="comment"></span><span class="comment">//</span></div>
62
<div class="line"><a name="l00037"></a><span class="lineno"> 37</span> <span class="comment">// PEAK DETECTION OF FOURIER TRANSFORME MS INSTRUMENT DATA</span></div>
63
<div class="line"><a name="l00038"></a><span class="lineno"> 38</span> <span class="comment">//</span></div>
64
<div class="line"><a name="l00039"></a><span class="lineno"> 39</span> <span class="comment">// written by Markus Mueller, markus.mueller@imsb.biol.ethz.ch</span></div>
65
<div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="comment">// and Lukas Mueller, Lukas.Mueller@imsb.biol.ethz.ch</span></div>
66
<div class="line"><a name="l00041"></a><span class="lineno"> 41</span> <span class="comment">// October 2005</span></div>
67
<div class="line"><a name="l00042"></a><span class="lineno"> 42</span> <span class="comment">//</span></div>
68
<div class="line"><a name="l00043"></a><span class="lineno"> 43</span> <span class="comment">// Ported to OpenMS by Florian Zeller, florian.zeller@bsse.ethz.ch</span></div>
69
<div class="line"><a name="l00044"></a><span class="lineno"> 44</span> <span class="comment">// December 2010</span></div>
70
<div class="line"><a name="l00045"></a><span class="lineno"> 45</span> <span class="comment">//</span></div>
71
<div class="line"><a name="l00046"></a><span class="lineno"> 46</span> <span class="comment">// Group of Prof. Ruedi Aebersold, IMSB, ETH Hoenggerberg, Zurich</span></div>
72
<div class="line"><a name="l00047"></a><span class="lineno"> 47</span> <span class="comment">//</span></div>
73
<div class="line"><a name="l00048"></a><span class="lineno"> 48</span> <span class="comment">//</span></div>
74
<div class="line"><a name="l00049"></a><span class="lineno"> 49</span> </div>
75
<div class="line"><a name="l00050"></a><span class="lineno"> 50</span> <span class="preprocessor">#ifndef OPENMS_TRANSFORMATIONS_FEATUREFINDER_SUPERHIRN_LCELUTIONPEAK_H</span></div>
76
<div class="line"><a name="l00051"></a><span class="lineno"> 51</span> <span class="preprocessor"></span><span class="preprocessor">#define OPENMS_TRANSFORMATIONS_FEATUREFINDER_SUPERHIRN_LCELUTIONPEAK_H</span></div>
77
<div class="line"><a name="l00052"></a><span class="lineno"> 52</span> <span class="preprocessor"></span></div>
78
<div class="line"><a name="l00053"></a><span class="lineno"> 53</span> <span class="preprocessor">#include <vector></span></div>
79
<div class="line"><a name="l00054"></a><span class="lineno"> 54</span> <span class="preprocessor">#include <map></span></div>
80
<div class="line"><a name="l00055"></a><span class="lineno"> 55</span> <span class="preprocessor">#include <<a class="code" href="ConsensusIsotopePattern_8h.html">OpenMS/TRANSFORMATIONS/FEATUREFINDER/SUPERHIRN/ConsensusIsotopePattern.h</a>></span></div>
81
<div class="line"><a name="l00056"></a><span class="lineno"> 56</span> </div>
82
<div class="line"><a name="l00057"></a><span class="lineno"> 57</span> <span class="keyword">namespace </span>OpenMS</div>
83
<div class="line"><a name="l00058"></a><span class="lineno"> 58</span> {</div>
84
<div class="line"><a name="l00059"></a><span class="lineno"> 59</span> </div>
85
<div class="line"><a name="l00060"></a><span class="lineno"><a class="line" href="namespaceOpenMS.html#af18558f60329d153e5f439e6b6cbc6fa"> 60</a></span>  <span class="keyword">typedef</span> std::multimap<int, MSPeak> <a class="code" href="namespaceOpenMS.html#af18558f60329d153e5f439e6b6cbc6fa">elution_peak</a>;</div>
86
<div class="line"><a name="l00061"></a><span class="lineno"><a class="line" href="namespaceOpenMS.html#ab69ab1a8bcf64e4e36a57672502f93dc"> 61</a></span>  <span class="keyword">typedef</span> std::vector<elution_peak> <a class="code" href="namespaceOpenMS.html#ab69ab1a8bcf64e4e36a57672502f93dc">MZ_series</a>;</div>
87
<div class="line"><a name="l00062"></a><span class="lineno"><a class="line" href="namespaceOpenMS.html#a79e6b2973636a97ad0228a737ddcbed6"> 62</a></span>  <span class="keyword">typedef</span> std::vector<elution_peak>::iterator <a class="code" href="namespaceOpenMS.html#a79e6b2973636a97ad0228a737ddcbed6">MZ_series_ITERATOR</a>;</div>
88
<div class="line"><a name="l00063"></a><span class="lineno"><a class="line" href="namespaceOpenMS.html#a86f33425d6d3c820cf964cacc9a3fd34"> 63</a></span>  <span class="keyword">typedef</span> std::multimap<int, MSPeak>::iterator <a class="code" href="namespaceOpenMS.html#a86f33425d6d3c820cf964cacc9a3fd34">SIGNAL_iterator</a>;</div>
89
<div class="line"><a name="l00064"></a><span class="lineno"> 64</span> </div>
90
<div class="line"><a name="l00065"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCElutionPeak.html"> 65</a></span>  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1LCElutionPeak.html">LCElutionPeak</a></div>
91
<div class="line"><a name="l00066"></a><span class="lineno"> 66</span>  {</div>
92
<div class="line"><a name="l00067"></a><span class="lineno"> 67</span> </div>
93
<div class="line"><a name="l00069"></a><span class="lineno"> 69</span>  <span class="comment">// declaration of the private members:</span></div>
94
<div class="line"><a name="l00070"></a><span class="lineno"> 70</span> </div>
95
<div class="line"><a name="l00071"></a><span class="lineno"> 71</span> <span class="keyword">private</span>:</div>
96
<div class="line"><a name="l00072"></a><span class="lineno"> 72</span> </div>
97
<div class="line"><a name="l00073"></a><span class="lineno"> 73</span>  <span class="comment">// isotopic pattern:</span></div>
98
<div class="line"><a name="l00074"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCElutionPeak.html#aa624be0a99fd8e5e73fc019d3f5790e1"> 74</a></span>  <a class="code" href="classOpenMS_1_1ConsensusIsotopePattern.html">ConsensusIsotopePattern</a> * <a class="code" href="classOpenMS_1_1LCElutionPeak.html#aa624be0a99fd8e5e73fc019d3f5790e1">isotopePattern</a>;</div>
99
<div class="line"><a name="l00075"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCElutionPeak.html#ae08b9afa83396a99cf29848c902b1b5f"> 75</a></span>  <span class="keywordtype">int</span> <a class="code" href="classOpenMS_1_1LCElutionPeak.html#ae08b9afa83396a99cf29848c902b1b5f">fNrIsotopes</a>;</div>
100
<div class="line"><a name="l00076"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCElutionPeak.html#a3e554fdf19c9a25b10ec1264bf68bec8"> 76</a></span>  <span class="keywordtype">double</span> <a class="code" href="classOpenMS_1_1LCElutionPeak.html#a3e554fdf19c9a25b10ec1264bf68bec8">f_observed_Mass</a>;</div>
101
<div class="line"><a name="l00077"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCElutionPeak.html#a508b1c44a0cfd87efba4d6a2febb4231"> 77</a></span>  <span class="keywordtype">double</span> <a class="code" href="classOpenMS_1_1LCElutionPeak.html#a508b1c44a0cfd87efba4d6a2febb4231">fIsotopMass</a>;</div>
102
<div class="line"><a name="l00078"></a><span class="lineno"> 78</span> </div>
103
<div class="line"><a name="l00079"></a><span class="lineno"> 79</span> <span class="keyword">protected</span>:</div>
104
<div class="line"><a name="l00080"></a><span class="lineno"> 80</span> </div>
105
<div class="line"><a name="l00081"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCElutionPeak.html#ac51a16752e2e401cad22b5f6c2665924"> 81</a></span>  <span class="keywordtype">double</span> <a class="code" href="classOpenMS_1_1LCElutionPeak.html#ac51a16752e2e401cad22b5f6c2665924">fMonoMass</a>;</div>
106
<div class="line"><a name="l00082"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCElutionPeak.html#a7a3ac2f5ce9bd348d2fde4597d7c8bed"> 82</a></span>  <span class="keywordtype">double</span> <a class="code" href="classOpenMS_1_1LCElutionPeak.html#a7a3ac2f5ce9bd348d2fde4597d7c8bed">fVolume</a>;</div>
107
<div class="line"><a name="l00083"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCElutionPeak.html#a2e1ce7191795f93224d0c7c556dc54fa"> 83</a></span>  <span class="keywordtype">int</span> <a class="code" href="classOpenMS_1_1LCElutionPeak.html#a2e1ce7191795f93224d0c7c556dc54fa">fCharge</a>;</div>
108
<div class="line"><a name="l00084"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCElutionPeak.html#a6cf5b2361685fd6e7fde43a96498ce9e"> 84</a></span>  <span class="keywordtype">int</span> <a class="code" href="classOpenMS_1_1LCElutionPeak.html#a6cf5b2361685fd6e7fde43a96498ce9e">fScanNumberStart</a>;</div>
109
<div class="line"><a name="l00085"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCElutionPeak.html#aa35ecbe8a1c84b062addb6b6255b2fb2"> 85</a></span>  <span class="keywordtype">int</span> <a class="code" href="classOpenMS_1_1LCElutionPeak.html#aa35ecbe8a1c84b062addb6b6255b2fb2">fScanNumberApex</a>;</div>
110
<div class="line"><a name="l00086"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCElutionPeak.html#af77af24ac504f5f44a91f1ca24f34864"> 86</a></span>  <span class="keywordtype">int</span> <a class="code" href="classOpenMS_1_1LCElutionPeak.html#af77af24ac504f5f44a91f1ca24f34864">fScanNumberEnd</a>;</div>
111
<div class="line"><a name="l00087"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCElutionPeak.html#a99157c03ee77754d15cb31611586265d"> 87</a></span>  <span class="keywordtype">double</span> <a class="code" href="classOpenMS_1_1LCElutionPeak.html#a99157c03ee77754d15cb31611586265d">fapex_intensity</a>;</div>
112
<div class="line"><a name="l00088"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCElutionPeak.html#a44cd080df0f59602c14eb29fb6128cc5"> 88</a></span>  <span class="keywordtype">double</span> <a class="code" href="classOpenMS_1_1LCElutionPeak.html#a44cd080df0f59602c14eb29fb6128cc5">fRT</a>;</div>
113
<div class="line"><a name="l00089"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCElutionPeak.html#a312f7c201776e27ecd97e85a0e7f5024"> 89</a></span>  <span class="keywordtype">double</span> <a class="code" href="classOpenMS_1_1LCElutionPeak.html#a312f7c201776e27ecd97e85a0e7f5024">fStartTR</a>;</div>
114
<div class="line"><a name="l00090"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCElutionPeak.html#a204b174e9a86216f70de4eb0aa71fda6"> 90</a></span>  <span class="keywordtype">double</span> <a class="code" href="classOpenMS_1_1LCElutionPeak.html#a204b174e9a86216f70de4eb0aa71fda6">fEndTR</a>;</div>
115
<div class="line"><a name="l00091"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCElutionPeak.html#a02910972b1977ebde5a95e3b86d7722b"> 91</a></span>  <span class="keywordtype">double</span> <a class="code" href="classOpenMS_1_1LCElutionPeak.html#a02910972b1977ebde5a95e3b86d7722b">fpeak_area</a>;</div>
116
<div class="line"><a name="l00092"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCElutionPeak.html#a64013730f99f52c28ff480e63b75ea78"> 92</a></span>  <span class="keywordtype">double</span> <a class="code" href="classOpenMS_1_1LCElutionPeak.html#a64013730f99f52c28ff480e63b75ea78">fSignalToNoise</a>;</div>
117
<div class="line"><a name="l00093"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCElutionPeak.html#addc9ab666f80e876c8571db7f3a8e069"> 93</a></span>  <span class="keywordtype">double</span> <a class="code" href="classOpenMS_1_1LCElutionPeak.html#addc9ab666f80e876c8571db7f3a8e069">fSNIntensityThreshold</a>;</div>
118
<div class="line"><a name="l00094"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCElutionPeak.html#a721772ba0ec677852bf5c94ae467c195"> 94</a></span>  <a class="code" href="classOpenMS_1_1MSPeak.html">MSPeak</a> * <a class="code" href="classOpenMS_1_1LCElutionPeak.html#a721772ba0ec677852bf5c94ae467c195">APEX</a>;</div>
119
<div class="line"><a name="l00095"></a><span class="lineno"> 95</span> </div>
120
<div class="line"><a name="l00096"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCElutionPeak.html#aae48edd486239c935bb45c15712fa9e5"> 96</a></span>  std::string <a class="code" href="classOpenMS_1_1LCElutionPeak.html#aae48edd486239c935bb45c15712fa9e5">elutionPeakExtraInfo</a>;</div>
121
<div class="line"><a name="l00097"></a><span class="lineno"> 97</span> </div>
122
<div class="line"><a name="l00098"></a><span class="lineno"> 98</span>  <span class="comment">// the raw signals assigned to this peak</span></div>
123
<div class="line"><a name="l00099"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCElutionPeak.html#abdecd7687dcc666c696fca36cb7ee768"> 99</a></span>  std::multimap<int, MSPeak> <a class="code" href="classOpenMS_1_1LCElutionPeak.html#abdecd7687dcc666c696fca36cb7ee768">intens_signals</a>;</div>
124
<div class="line"><a name="l00100"></a><span class="lineno"> 100</span>  <span class="comment">//multimap<int, MSPeak> raw_intens_signals;</span></div>
125
<div class="line"><a name="l00101"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCElutionPeak.html#aa34a1124f2a9332ea102d2cab19580c2"> 101</a></span>  std::multimap<int, int> <a class="code" href="classOpenMS_1_1LCElutionPeak.html#aa34a1124f2a9332ea102d2cab19580c2">CHRG_MAP</a>;</div>
126
<div class="line"><a name="l00102"></a><span class="lineno"> 102</span> </div>
127
<div class="line"><a name="l00104"></a><span class="lineno"> 104</span>  <span class="comment">// declaration of the public members:</span></div>
128
<div class="line"><a name="l00105"></a><span class="lineno"> 105</span> </div>
129
<div class="line"><a name="l00106"></a><span class="lineno"> 106</span> <span class="keyword">public</span>:</div>
130
<div class="line"><a name="l00107"></a><span class="lineno"> 107</span> </div>
131
<div class="line"><a name="l00108"></a><span class="lineno"> 108</span>  <span class="comment">// parameters to debug a ceratain mass range</span></div>
132
<div class="line"><a name="l00109"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCElutionPeak.html#aeacd03494bac7bbad33feadfb81e613a"> 109</a></span>  <span class="keyword">static</span> <span class="keywordtype">double</span> <a class="code" href="classOpenMS_1_1LCElutionPeak.html#aeacd03494bac7bbad33feadfb81e613a">DEBUG_MASS_START</a>;</div>
133
<div class="line"><a name="l00110"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCElutionPeak.html#acb7760252e63bf27414aeb15575b3b68"> 110</a></span>  <span class="keyword">static</span> <span class="keywordtype">double</span> <a class="code" href="classOpenMS_1_1LCElutionPeak.html#acb7760252e63bf27414aeb15575b3b68">DEBUG_MASS_END</a>;</div>
134
<div class="line"><a name="l00111"></a><span class="lineno"> 111</span> </div>
135
<div class="line"><a name="l00112"></a><span class="lineno"> 112</span>  <span class="comment">// cut off, where everything small than this precentile of the</span></div>
136
<div class="line"><a name="l00113"></a><span class="lineno"> 113</span>  <span class="comment">// apex is discarded</span></div>
137
<div class="line"><a name="l00114"></a><span class="lineno"> 114</span>  <span class="comment">// static float intensity_apex_percentil_cutoff;</span></div>
138
<div class="line"><a name="l00115"></a><span class="lineno"> 115</span> </div>
139
<div class="line"><a name="l00116"></a><span class="lineno"> 116</span>  <span class="comment">// resolution of the retention time, for peak area copmuting:</span></div>
140
<div class="line"><a name="l00117"></a><span class="lineno"> 117</span>  <span class="comment">// static float TR_RESOLUTION;</span></div>
141
<div class="line"><a name="l00118"></a><span class="lineno"> 118</span> </div>
142
<div class="line"><a name="l00119"></a><span class="lineno"> 119</span>  <span class="comment">// class destructor</span></div>
143
<div class="line"><a name="l00120"></a><span class="lineno"> 120</span>  ~<a class="code" href="classOpenMS_1_1LCElutionPeak.html">LCElutionPeak</a>();</div>
144
<div class="line"><a name="l00121"></a><span class="lineno"> 121</span> </div>
145
<div class="line"><a name="l00122"></a><span class="lineno"> 122</span>  <span class="comment">// class constructor</span></div>
146
<div class="line"><a name="l00123"></a><span class="lineno"> 123</span>  <a class="code" href="classOpenMS_1_1LCElutionPeak.html">LCElutionPeak</a>();</div>
147
<div class="line"><a name="l00124"></a><span class="lineno"> 124</span>  <span class="comment">// class constructor</span></div>
148
<div class="line"><a name="l00125"></a><span class="lineno"> 125</span>  <a class="code" href="classOpenMS_1_1LCElutionPeak.html">LCElutionPeak</a>(<a class="code" href="namespaceOpenMS.html#a79e6b2973636a97ad0228a737ddcbed6">MZ_series_ITERATOR</a>, <span class="keywordtype">double</span>);</div>
149
<div class="line"><a name="l00126"></a><span class="lineno"> 126</span>  <span class="comment">// class copy constructor</span></div>
150
<div class="line"><a name="l00127"></a><span class="lineno"> 127</span>  <a class="code" href="classOpenMS_1_1LCElutionPeak.html">LCElutionPeak</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1LCElutionPeak.html">LCElutionPeak</a> &);</div>
151
<div class="line"><a name="l00128"></a><span class="lineno"> 128</span>  <span class="comment">// constructor for the object feature:</span></div>
152
<div class="line"><a name="l00129"></a><span class="lineno"> 129</span>  <a class="code" href="classOpenMS_1_1LCElutionPeak.html">LCElutionPeak</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1LCElutionPeak.html">LCElutionPeak</a> *);</div>
153
<div class="line"><a name="l00130"></a><span class="lineno"> 130</span> </div>
154
<div class="line"><a name="l00132"></a><span class="lineno"> 132</span>  <span class="comment">// Analyze the LC elution peak</span></div>
155
<div class="line"><a name="l00133"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCElutionPeak.html#a6fec4c9e10aa7806d2e811e5f59f2219"> 133</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1LCElutionPeak.html#a6fec4c9e10aa7806d2e811e5f59f2219">analyzeLCElutionPeak</a>()</div>
156
<div class="line"><a name="l00134"></a><span class="lineno"> 134</span>  {</div>
157
<div class="line"><a name="l00135"></a><span class="lineno"> 135</span> </div>
158
<div class="line"><a name="l00136"></a><span class="lineno"> 136</span>  <span class="keywordflow">if</span> (get_nb_ms_peaks() > 1)</div>
159
<div class="line"><a name="l00137"></a><span class="lineno"> 137</span>  {</div>
160
<div class="line"><a name="l00138"></a><span class="lineno"> 138</span> </div>
161
<div class="line"><a name="l00139"></a><span class="lineno"> 139</span>  CHRG_MAP.clear();</div>
162
<div class="line"><a name="l00140"></a><span class="lineno"> 140</span> </div>
163
<div class="line"><a name="l00141"></a><span class="lineno"> 141</span>  <span class="comment">// determine the intensity background baseline based on S/N</span></div>
164
<div class="line"><a name="l00142"></a><span class="lineno"> 142</span>  <span class="comment">// value:</span></div>
165
<div class="line"><a name="l00143"></a><span class="lineno"> 143</span>  setSNIntensityThreshold();</div>
166
<div class="line"><a name="l00144"></a><span class="lineno"> 144</span> </div>
167
<div class="line"><a name="l00145"></a><span class="lineno"> 145</span>  <span class="comment">// Compute a varietiy of parameters for the LC elution peak</span></div>
168
<div class="line"><a name="l00146"></a><span class="lineno"> 146</span>  computeLCElutionPeakParameters();</div>
169
<div class="line"><a name="l00147"></a><span class="lineno"> 147</span> </div>
170
<div class="line"><a name="l00148"></a><span class="lineno"> 148</span>  <span class="comment">// define parameters such as chrg, score</span></div>
171
<div class="line"><a name="l00149"></a><span class="lineno"> 149</span>  compute_CHRG();</div>
172
<div class="line"><a name="l00150"></a><span class="lineno"> 150</span> </div>
173
<div class="line"><a name="l00151"></a><span class="lineno"> 151</span>  <span class="comment">// create the consensus pattern:</span></div>
174
<div class="line"><a name="l00152"></a><span class="lineno"> 152</span>  createConsensIsotopPattern();</div>
175
<div class="line"><a name="l00153"></a><span class="lineno"> 153</span>  }</div>
176
<div class="line"><a name="l00154"></a><span class="lineno"> 154</span>  <span class="keywordflow">else</span></div>
177
<div class="line"><a name="l00155"></a><span class="lineno"> 155</span>  {</div>
178
<div class="line"><a name="l00156"></a><span class="lineno"> 156</span>  defineLCElutionPeakParametersFromMSPeak();</div>
179
<div class="line"><a name="l00157"></a><span class="lineno"> 157</span>  }</div>
180
<div class="line"><a name="l00158"></a><span class="lineno"> 158</span>  }</div>
181
<div class="line"><a name="l00159"></a><span class="lineno"> 159</span> </div>
182
<div class="line"><a name="l00161"></a><span class="lineno"> 161</span>  <span class="comment">// determine the intensity background baseline based on S/N</span></div>
183
<div class="line"><a name="l00162"></a><span class="lineno"> 162</span>  <span class="comment">// value:</span></div>
184
<div class="line"><a name="l00163"></a><span class="lineno"> 163</span>  <span class="keywordtype">void</span> setSNIntensityThreshold();</div>
185
<div class="line"><a name="l00164"></a><span class="lineno"> 164</span> </div>
186
<div class="line"><a name="l00166"></a><span class="lineno"> 166</span>  <span class="comment">// Compute a varietiy of parameters for the LC elution peak</span></div>
187
<div class="line"><a name="l00167"></a><span class="lineno"> 167</span>  <span class="keywordtype">void</span> computeLCElutionPeakParameters();</div>
188
<div class="line"><a name="l00168"></a><span class="lineno"> 168</span> </div>
189
<div class="line"><a name="l00169"></a><span class="lineno"> 169</span>  <span class="comment">// removes background peaks and computes the total peak area:</span></div>
190
<div class="line"><a name="l00170"></a><span class="lineno"> 170</span>  <span class="comment">// void compute_LC_peak_area();</span></div>
191
<div class="line"><a name="l00171"></a><span class="lineno"> 171</span>  <span class="comment">// computes the area of between 2 peaks:</span></div>
192
<div class="line"><a name="l00172"></a><span class="lineno"> 172</span>  <span class="keywordtype">double</span> compute_delta_area(<span class="keywordtype">double</span>, <span class="keywordtype">double</span>, <span class="keywordtype">double</span>, <span class="keywordtype">double</span>);</div>
193
<div class="line"><a name="l00173"></a><span class="lineno"> 173</span>  <span class="comment">// define the apex into the elution profile::</span></div>
194
<div class="line"><a name="l00174"></a><span class="lineno"> 174</span>  <span class="comment">// void define_apex();</span></div>
195
<div class="line"><a name="l00175"></a><span class="lineno"> 175</span>  <span class="comment">// removes peaks which have lower intensity than x percentile</span></div>
196
<div class="line"><a name="l00176"></a><span class="lineno"> 176</span>  <span class="comment">// of the apex:</span></div>
197
<div class="line"><a name="l00177"></a><span class="lineno"> 177</span>  <span class="keywordtype">void</span> remove_background_peak();</div>
198
<div class="line"><a name="l00178"></a><span class="lineno"> 178</span>  <span class="comment">// compute the charge state of the LC peak</span></div>
199
<div class="line"><a name="l00179"></a><span class="lineno"> 179</span>  <span class="keywordtype">void</span> compute_CHRG();</div>
200
<div class="line"><a name="l00180"></a><span class="lineno"> 180</span>  <span class="comment">// compute the score of the LC peak:</span></div>
201
<div class="line"><a name="l00181"></a><span class="lineno"> 181</span>  <span class="comment">//void compute_SCORE_and_SN();</span></div>
202
<div class="line"><a name="l00182"></a><span class="lineno"> 182</span>  <span class="comment">// define all required peak parameters from a single MS peak:</span></div>
203
<div class="line"><a name="l00183"></a><span class="lineno"> 183</span>  <span class="keywordtype">void</span> defineLCElutionPeakParametersFromMSPeak();</div>
204
<div class="line"><a name="l00185"></a><span class="lineno"> 185</span> </div>
205
<div class="line"><a name="l00187"></a><span class="lineno"> 187</span>  <span class="comment">// print all monositopic peak cluster along the LC profile:</span></div>
206
<div class="line"><a name="l00188"></a><span class="lineno"> 188</span>  <span class="keywordtype">void</span> createConsensIsotopPattern();</div>
207
<div class="line"><a name="l00189"></a><span class="lineno"> 189</span> </div>
208
<div class="line"><a name="l00190"></a><span class="lineno"> 190</span>  <span class="comment">// print the elution profile from a peak:</span></div>
209
<div class="line"><a name="l00191"></a><span class="lineno"> 191</span>  <span class="keywordtype">void</span> print_profile(std::ofstream *);</div>
210
<div class="line"><a name="l00192"></a><span class="lineno"> 192</span>  <span class="comment">// find the closest existing mz peak in the elution profile:</span></div>
211
<div class="line"><a name="l00193"></a><span class="lineno"> 193</span>  <a class="code" href="classOpenMS_1_1MSPeak.html">MSPeak</a> * find_true_peak(<span class="keywordtype">float</span>);</div>
212
<div class="line"><a name="l00194"></a><span class="lineno"> 194</span>  <span class="comment">// print the elution profile from a peak:</span></div>
213
<div class="line"><a name="l00195"></a><span class="lineno"> 195</span>  <span class="keywordtype">void</span> show_info();</div>
214
<div class="line"><a name="l00196"></a><span class="lineno"> 196</span> </div>
215
<div class="line"><a name="l00198"></a><span class="lineno"> 198</span>  <span class="comment">// overload operators:</span></div>
216
<div class="line"><a name="l00199"></a><span class="lineno"> 199</span>  <a class="code" href="classOpenMS_1_1LCElutionPeak.html">LCElutionPeak</a> & operator=(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1LCElutionPeak.html">LCElutionPeak</a> &);</div>
217
<div class="line"><a name="l00200"></a><span class="lineno"> 200</span>  <a class="code" href="classOpenMS_1_1LCElutionPeak.html">LCElutionPeak</a> & operator<=(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1LCElutionPeak.html">LCElutionPeak</a> &);</div>
218
<div class="line"><a name="l00201"></a><span class="lineno"> 201</span>  <a class="code" href="classOpenMS_1_1LCElutionPeak.html">LCElutionPeak</a> & operator>=(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1LCElutionPeak.html">LCElutionPeak</a> &);</div>
219
<div class="line"><a name="l00202"></a><span class="lineno"> 202</span>  <a class="code" href="classOpenMS_1_1LCElutionPeak.html">LCElutionPeak</a> & operator<(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1LCElutionPeak.html">LCElutionPeak</a> &);</div>
220
<div class="line"><a name="l00203"></a><span class="lineno"> 203</span>  <a class="code" href="classOpenMS_1_1LCElutionPeak.html">LCElutionPeak</a> & operator>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1LCElutionPeak.html">LCElutionPeak</a> &);</div>
221
<div class="line"><a name="l00204"></a><span class="lineno"> 204</span> </div>
222
<div class="line"><a name="l00206"></a><span class="lineno"> 206</span>  <span class="comment">// print all monositopic peak cluster along the LC profile:</span></div>
223
<div class="line"><a name="l00207"></a><span class="lineno"> 207</span>  <span class="comment">//void printIsotopClusters();</span></div>
224
<div class="line"><a name="l00208"></a><span class="lineno"> 208</span>  <span class="comment">// print the consensus isotope pattern:</span></div>
225
<div class="line"><a name="l00209"></a><span class="lineno"> 209</span>  <span class="comment">//void printConsensIsotopPattern();</span></div>
226
<div class="line"><a name="l00210"></a><span class="lineno"> 210</span> </div>
227
<div class="line"><a name="l00211"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCElutionPeak.html#ac81d671afeef6f8fb49a01556d7ca47c"> 211</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1LCElutionPeak.html#ac81d671afeef6f8fb49a01556d7ca47c">setElutionPeakExtraInfo</a>(std::string in)</div>
228
<div class="line"><a name="l00212"></a><span class="lineno"> 212</span>  {</div>
229
<div class="line"><a name="l00213"></a><span class="lineno"> 213</span>  elutionPeakExtraInfo = in;</div>
230
<div class="line"><a name="l00214"></a><span class="lineno"> 214</span>  }</div>
231
<div class="line"><a name="l00215"></a><span class="lineno"> 215</span> </div>
232
<div class="line"><a name="l00216"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCElutionPeak.html#a364c5a3b05ab685c42af06bc462b3344"> 216</a></span>  std::string <a class="code" href="classOpenMS_1_1LCElutionPeak.html#a364c5a3b05ab685c42af06bc462b3344">getElutionPeakExtraInfo</a>()</div>
233
<div class="line"><a name="l00217"></a><span class="lineno"> 217</span>  {</div>
234
<div class="line"><a name="l00218"></a><span class="lineno"> 218</span>  <span class="keywordflow">return</span> elutionPeakExtraInfo;</div>
235
<div class="line"><a name="l00219"></a><span class="lineno"> 219</span>  }</div>
236
<div class="line"><a name="l00220"></a><span class="lineno"> 220</span> </div>
237
<div class="line"><a name="l00222"></a><span class="lineno"> 222</span>  <span class="comment">// start here all the get / set</span></div>
238
<div class="line"><a name="l00223"></a><span class="lineno"> 223</span>  <span class="comment">// function to access the</span></div>
239
<div class="line"><a name="l00224"></a><span class="lineno"> 224</span>  <span class="comment">// variables of the class</span></div>
240
<div class="line"><a name="l00225"></a><span class="lineno"> 225</span> </div>
241
<div class="line"><a name="l00227"></a><span class="lineno"> 227</span>  <span class="comment">// access signal_intens map:</span></div>
242
<div class="line"><a name="l00228"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCElutionPeak.html#aaab6cb4b26d8f84a94eee092b755c66b"> 228</a></span>  <a class="code" href="namespaceOpenMS.html#a86f33425d6d3c820cf964cacc9a3fd34">SIGNAL_iterator</a> <a class="code" href="classOpenMS_1_1LCElutionPeak.html#aaab6cb4b26d8f84a94eee092b755c66b">get_signal_list_start</a>()</div>
243
<div class="line"><a name="l00229"></a><span class="lineno"> 229</span>  {</div>
244
<div class="line"><a name="l00230"></a><span class="lineno"> 230</span>  <span class="keywordflow">return</span> intens_signals.begin();</div>
245
<div class="line"><a name="l00231"></a><span class="lineno"> 231</span>  }</div>
246
<div class="line"><a name="l00232"></a><span class="lineno"> 232</span> </div>
247
<div class="line"><a name="l00233"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCElutionPeak.html#a47e3af93b063da2448711d8a8f250a1a"> 233</a></span>  <a class="code" href="namespaceOpenMS.html#a86f33425d6d3c820cf964cacc9a3fd34">SIGNAL_iterator</a> <a class="code" href="classOpenMS_1_1LCElutionPeak.html#a47e3af93b063da2448711d8a8f250a1a">get_signal_list_end</a>()</div>
248
<div class="line"><a name="l00234"></a><span class="lineno"> 234</span>  {</div>
249
<div class="line"><a name="l00235"></a><span class="lineno"> 235</span>  <span class="keywordflow">return</span> intens_signals.end();</div>
250
<div class="line"><a name="l00236"></a><span class="lineno"> 236</span>  }</div>
251
<div class="line"><a name="l00237"></a><span class="lineno"> 237</span> </div>
252
<div class="line"><a name="l00239"></a><span class="lineno"> 239</span>  <span class="comment">// access the raw signal intens map:</span></div>
253
<div class="line"><a name="l00240"></a><span class="lineno"> 240</span>  <span class="comment">//SIGNAL_iterator get_raw_signal_list_start(){return raw_intens_signals.begin();};</span></div>
254
<div class="line"><a name="l00241"></a><span class="lineno"> 241</span>  <span class="comment">//SIGNAL_iterator get_raw_signal_list_end(){return raw_intens_signals.end();};</span></div>
255
<div class="line"><a name="l00242"></a><span class="lineno"> 242</span> </div>
256
<div class="line"><a name="l00243"></a><span class="lineno"> 243</span>  <span class="comment">// update the retention time by the current tmp_scan_apex:</span></div>
257
<div class="line"><a name="l00244"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCElutionPeak.html#a49294cdec251db872fb2b9355a697057"> 244</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1LCElutionPeak.html#a49294cdec251db872fb2b9355a697057">set_apex_retention_time</a>(<span class="keywordtype">double</span> IN)</div>
258
<div class="line"><a name="l00245"></a><span class="lineno"> 245</span>  {</div>
259
<div class="line"><a name="l00246"></a><span class="lineno"> 246</span>  fRT = IN;</div>
260
<div class="line"><a name="l00247"></a><span class="lineno"> 247</span>  }</div>
261
<div class="line"><a name="l00248"></a><span class="lineno"> 248</span> </div>
262
<div class="line"><a name="l00249"></a><span class="lineno"> 249</span>  <span class="comment">// to update the list of score and charge state:</span></div>
263
<div class="line"><a name="l00250"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCElutionPeak.html#a7c2cde6b2669674ee10ac27ed0b38f03"> 250</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1LCElutionPeak.html#a7c2cde6b2669674ee10ac27ed0b38f03">update_CHRGMAP</a>(<a class="code" href="classOpenMS_1_1MSPeak.html">MSPeak</a> * IN)</div>
264
<div class="line"><a name="l00251"></a><span class="lineno"> 251</span>  {</div>
265
<div class="line"><a name="l00252"></a><span class="lineno"> 252</span>  std::multimap<int, int>::iterator T = CHRG_MAP.find(IN-><a class="code" href="classOpenMS_1_1MSPeak.html#a56d6a680a88ac07ad6e23417cfbebb6f">get_charge_state</a>());</div>
266
<div class="line"><a name="l00253"></a><span class="lineno"> 253</span>  <span class="keywordflow">if</span> (T == CHRG_MAP.end())</div>
267
<div class="line"><a name="l00254"></a><span class="lineno"> 254</span>  {</div>
268
<div class="line"><a name="l00255"></a><span class="lineno"> 255</span>  CHRG_MAP.insert(std::make_pair(IN-><a class="code" href="classOpenMS_1_1MSPeak.html#a56d6a680a88ac07ad6e23417cfbebb6f">get_charge_state</a>(), 1));</div>
269
<div class="line"><a name="l00256"></a><span class="lineno"> 256</span>  }</div>
270
<div class="line"><a name="l00257"></a><span class="lineno"> 257</span>  <span class="keywordflow">else</span></div>
271
<div class="line"><a name="l00258"></a><span class="lineno"> 258</span>  {</div>
272
<div class="line"><a name="l00259"></a><span class="lineno"> 259</span>  (*T).second++;</div>
273
<div class="line"><a name="l00260"></a><span class="lineno"> 260</span>  }</div>
274
<div class="line"><a name="l00261"></a><span class="lineno"> 261</span>  }</div>
275
<div class="line"><a name="l00262"></a><span class="lineno"> 262</span> </div>
276
<div class="line"><a name="l00264"></a><span class="lineno"> 264</span>  <span class="comment">// get scan apex:</span></div>
277
<div class="line"><a name="l00265"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCElutionPeak.html#a1a0d8a914f8b9c1189829edcb142a93d"> 265</a></span>  <span class="keywordtype">int</span> <a class="code" href="classOpenMS_1_1LCElutionPeak.html#a1a0d8a914f8b9c1189829edcb142a93d">get_scan_apex</a>()</div>
278
<div class="line"><a name="l00266"></a><span class="lineno"> 266</span>  {</div>
279
<div class="line"><a name="l00267"></a><span class="lineno"> 267</span>  <span class="keywordflow">return</span> fScanNumberApex;</div>
280
<div class="line"><a name="l00268"></a><span class="lineno"> 268</span>  }</div>
281
<div class="line"><a name="l00269"></a><span class="lineno"> 269</span> </div>
282
<div class="line"><a name="l00270"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCElutionPeak.html#ab812559cf209574e7cdc97e740d8600e"> 270</a></span>  <span class="keywordtype">double</span> <a class="code" href="classOpenMS_1_1LCElutionPeak.html#ab812559cf209574e7cdc97e740d8600e">get_apex_intensity</a>()</div>
283
<div class="line"><a name="l00271"></a><span class="lineno"> 271</span>  {</div>
284
<div class="line"><a name="l00272"></a><span class="lineno"> 272</span>  <span class="keywordflow">return</span> fapex_intensity;</div>
285
<div class="line"><a name="l00273"></a><span class="lineno"> 273</span>  }</div>
286
<div class="line"><a name="l00274"></a><span class="lineno"> 274</span> </div>
287
<div class="line"><a name="l00275"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCElutionPeak.html#a71bd48a0a57a43a9d57adb02cf478e47"> 275</a></span>  <span class="keywordtype">double</span> <a class="code" href="classOpenMS_1_1LCElutionPeak.html#a71bd48a0a57a43a9d57adb02cf478e47">get_apex_retention_time</a>()</div>
288
<div class="line"><a name="l00276"></a><span class="lineno"> 276</span>  {</div>
289
<div class="line"><a name="l00277"></a><span class="lineno"> 277</span>  <span class="keywordflow">return</span> fRT;</div>
290
<div class="line"><a name="l00278"></a><span class="lineno"> 278</span>  }</div>
291
<div class="line"><a name="l00279"></a><span class="lineno"> 279</span> </div>
292
<div class="line"><a name="l00280"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCElutionPeak.html#ab3d9ebea3826de1e67b776e6579f9af1"> 280</a></span>  <span class="keywordtype">double</span> <a class="code" href="classOpenMS_1_1LCElutionPeak.html#ab3d9ebea3826de1e67b776e6579f9af1">get_apex_MZ</a>()</div>
293
<div class="line"><a name="l00281"></a><span class="lineno"> 281</span>  {</div>
294
<div class="line"><a name="l00282"></a><span class="lineno"> 282</span>  <span class="keywordflow">return</span> get_MZ(get_scan_apex());</div>
295
<div class="line"><a name="l00283"></a><span class="lineno"> 283</span>  }</div>
296
<div class="line"><a name="l00284"></a><span class="lineno"> 284</span> </div>
297
<div class="line"><a name="l00286"></a><span class="lineno"> 286</span>  <span class="comment">// get an intensity of a ms_peak</span></div>
298
<div class="line"><a name="l00287"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCElutionPeak.html#aedffea12c90a091f3642027871dcce00"> 287</a></span>  <span class="keywordtype">float</span> <a class="code" href="classOpenMS_1_1LCElutionPeak.html#aedffea12c90a091f3642027871dcce00">get_intensity</a>(<span class="keywordtype">int</span> IN)</div>
299
<div class="line"><a name="l00288"></a><span class="lineno"> 288</span>  {</div>
300
<div class="line"><a name="l00289"></a><span class="lineno"> 289</span>  <span class="keywordflow">return</span> (*(intens_signals.find(IN))).second.get_intensity();</div>
301
<div class="line"><a name="l00290"></a><span class="lineno"> 290</span>  }</div>
302
<div class="line"><a name="l00291"></a><span class="lineno"> 291</span> </div>
303
<div class="line"><a name="l00292"></a><span class="lineno"> 292</span>  <span class="comment">// get the original M/Z of a ms_peak</span></div>
304
<div class="line"><a name="l00293"></a><span class="lineno"> 293</span>  <span class="keywordtype">double</span> get_MZ(<span class="keywordtype">int</span>);</div>
305
<div class="line"><a name="l00294"></a><span class="lineno"> 294</span> </div>
306
<div class="line"><a name="l00296"></a><span class="lineno"> 296</span>  <span class="comment">// get the total peak area:</span></div>
307
<div class="line"><a name="l00297"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCElutionPeak.html#a0f4a36df4dbdfd4a99366bcd24ae344f"> 297</a></span>  <span class="keywordtype">double</span> <a class="code" href="classOpenMS_1_1LCElutionPeak.html#a0f4a36df4dbdfd4a99366bcd24ae344f">get_total_peak_area</a>()</div>
308
<div class="line"><a name="l00298"></a><span class="lineno"> 298</span>  {</div>
309
<div class="line"><a name="l00299"></a><span class="lineno"> 299</span>  <span class="keywordflow">return</span> fpeak_area;</div>
310
<div class="line"><a name="l00300"></a><span class="lineno"> 300</span>  }</div>
311
<div class="line"><a name="l00301"></a><span class="lineno"> 301</span> </div>
312
<div class="line"><a name="l00303"></a><span class="lineno"> 303</span>  <span class="comment">// get start / end scan:</span></div>
313
<div class="line"><a name="l00304"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCElutionPeak.html#a5bdcacef9b788e18c0dd8c323186c390"> 304</a></span>  <span class="keywordtype">int</span> <a class="code" href="classOpenMS_1_1LCElutionPeak.html#a5bdcacef9b788e18c0dd8c323186c390">get_start_scan</a>()</div>
314
<div class="line"><a name="l00305"></a><span class="lineno"> 305</span>  {</div>
315
<div class="line"><a name="l00306"></a><span class="lineno"> 306</span>  <span class="keywordflow">return</span> fScanNumberStart;</div>
316
<div class="line"><a name="l00307"></a><span class="lineno"> 307</span>  }</div>
317
<div class="line"><a name="l00308"></a><span class="lineno"> 308</span> </div>
318
<div class="line"><a name="l00309"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCElutionPeak.html#aa5d97ba2d1f5db95c28860a4a2c5ce36"> 309</a></span>  <span class="keywordtype">int</span> <a class="code" href="classOpenMS_1_1LCElutionPeak.html#aa5d97ba2d1f5db95c28860a4a2c5ce36">get_end_scan</a>()</div>
319
<div class="line"><a name="l00310"></a><span class="lineno"> 310</span>  {</div>
320
<div class="line"><a name="l00311"></a><span class="lineno"> 311</span>  <span class="keywordflow">return</span> fScanNumberEnd;</div>
321
<div class="line"><a name="l00312"></a><span class="lineno"> 312</span>  }</div>
322
<div class="line"><a name="l00313"></a><span class="lineno"> 313</span> </div>
323
<div class="line"><a name="l00314"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCElutionPeak.html#a00e30b5e53b81e2957fb095937eab517"> 314</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1LCElutionPeak.html#a00e30b5e53b81e2957fb095937eab517">set_start_retention_time</a>(<span class="keywordtype">double</span> IN)</div>
324
<div class="line"><a name="l00315"></a><span class="lineno"> 315</span>  {</div>
325
<div class="line"><a name="l00316"></a><span class="lineno"> 316</span>  fStartTR = IN;</div>
326
<div class="line"><a name="l00317"></a><span class="lineno"> 317</span>  }</div>
327
<div class="line"><a name="l00318"></a><span class="lineno"> 318</span> </div>
328
<div class="line"><a name="l00319"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCElutionPeak.html#a1e5411880247f3ff9aed8ed75b23b7e4"> 319</a></span>  <span class="keywordtype">double</span> <a class="code" href="classOpenMS_1_1LCElutionPeak.html#a1e5411880247f3ff9aed8ed75b23b7e4">get_start_retention_time</a>()</div>
329
<div class="line"><a name="l00320"></a><span class="lineno"> 320</span>  {</div>
330
<div class="line"><a name="l00321"></a><span class="lineno"> 321</span>  <span class="keywordflow">return</span> fStartTR;</div>
331
<div class="line"><a name="l00322"></a><span class="lineno"> 322</span>  }</div>
332
<div class="line"><a name="l00323"></a><span class="lineno"> 323</span> </div>
333
<div class="line"><a name="l00324"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCElutionPeak.html#aa2f8a9c427c40f47910cdbfa03915cd8"> 324</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1LCElutionPeak.html#aa2f8a9c427c40f47910cdbfa03915cd8">set_end_retention_time</a>(<span class="keywordtype">double</span> IN)</div>
334
<div class="line"><a name="l00325"></a><span class="lineno"> 325</span>  {</div>
335
<div class="line"><a name="l00326"></a><span class="lineno"> 326</span>  fEndTR = IN;</div>
336
<div class="line"><a name="l00327"></a><span class="lineno"> 327</span>  }</div>
337
<div class="line"><a name="l00328"></a><span class="lineno"> 328</span> </div>
338
<div class="line"><a name="l00329"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCElutionPeak.html#a068dc107c061c02358e286404d49258a"> 329</a></span>  <span class="keywordtype">double</span> <a class="code" href="classOpenMS_1_1LCElutionPeak.html#a068dc107c061c02358e286404d49258a">get_end_retention_time</a>()</div>
339
<div class="line"><a name="l00330"></a><span class="lineno"> 330</span>  {</div>
340
<div class="line"><a name="l00331"></a><span class="lineno"> 331</span>  <span class="keywordflow">return</span> fEndTR;</div>
341
<div class="line"><a name="l00332"></a><span class="lineno"> 332</span>  }</div>
342
<div class="line"><a name="l00333"></a><span class="lineno"> 333</span> </div>
343
<div class="line"><a name="l00335"></a><span class="lineno"> 335</span>  <span class="comment">// get number of peaks in the elution profile:</span></div>
344
<div class="line"><a name="l00336"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCElutionPeak.html#a53ac877069cd954216c872fa56d301db"> 336</a></span>  <span class="keywordtype">int</span> <a class="code" href="classOpenMS_1_1LCElutionPeak.html#a53ac877069cd954216c872fa56d301db">get_nb_ms_peaks</a>()</div>
345
<div class="line"><a name="l00337"></a><span class="lineno"> 337</span>  {</div>
346
<div class="line"><a name="l00338"></a><span class="lineno"> 338</span>  <span class="keywordflow">return</span> (<span class="keywordtype">int</span>) intens_signals.size();</div>
347
<div class="line"><a name="l00339"></a><span class="lineno"> 339</span>  }</div>
348
<div class="line"><a name="l00340"></a><span class="lineno"> 340</span> </div>
349
<div class="line"><a name="l00342"></a><span class="lineno"> 342</span>  <span class="comment">// access teh charge state of the LC elutino peak:</span></div>
350
<div class="line"><a name="l00343"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCElutionPeak.html#a7cc0ff90acee6ff6f42056737fb78a22"> 343</a></span>  <span class="keywordtype">int</span> <a class="code" href="classOpenMS_1_1LCElutionPeak.html#a7cc0ff90acee6ff6f42056737fb78a22">get_charge_state</a>()</div>
351
<div class="line"><a name="l00344"></a><span class="lineno"> 344</span>  {</div>
352
<div class="line"><a name="l00345"></a><span class="lineno"> 345</span>  <span class="keywordflow">return</span> fCharge;</div>
353
<div class="line"><a name="l00346"></a><span class="lineno"> 346</span>  }</div>
354
<div class="line"><a name="l00347"></a><span class="lineno"> 347</span> </div>
355
<div class="line"><a name="l00349"></a><span class="lineno"> 349</span>  <span class="comment">// get signal to noise ratio:</span></div>
356
<div class="line"><a name="l00350"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCElutionPeak.html#a4bb41c31d39852daaa13eb35f5f04b23"> 350</a></span>  <span class="keywordtype">double</span> <a class="code" href="classOpenMS_1_1LCElutionPeak.html#a4bb41c31d39852daaa13eb35f5f04b23">getSignalToNoise</a>()</div>
357
<div class="line"><a name="l00351"></a><span class="lineno"> 351</span>  {</div>
358
<div class="line"><a name="l00352"></a><span class="lineno"> 352</span>  <span class="keywordflow">return</span> fSignalToNoise;</div>
359
<div class="line"><a name="l00353"></a><span class="lineno"> 353</span>  }</div>
360
<div class="line"><a name="l00354"></a><span class="lineno"> 354</span> </div>
361
<div class="line"><a name="l00355"></a><span class="lineno"><a class="line" href="classOpenMS_1_1LCElutionPeak.html#a9161872721a7fda574c3e2133d69a9a9"> 355</a></span>  <span class="keywordtype">double</span> <a class="code" href="classOpenMS_1_1LCElutionPeak.html#a9161872721a7fda574c3e2133d69a9a9">getSignalToNoiseBackground</a>()</div>
362
<div class="line"><a name="l00356"></a><span class="lineno"> 356</span>  {</div>
363
<div class="line"><a name="l00357"></a><span class="lineno"> 357</span>  <span class="keywordflow">return</span> fSNIntensityThreshold;</div>
364
<div class="line"><a name="l00358"></a><span class="lineno"> 358</span>  }</div>
365
<div class="line"><a name="l00359"></a><span class="lineno"> 359</span> </div>
366
<div class="line"><a name="l00360"></a><span class="lineno"> 360</span>  };</div>
367
<div class="line"><a name="l00361"></a><span class="lineno"> 361</span> </div>
368
<div class="line"><a name="l00362"></a><span class="lineno"> 362</span> } <span class="comment">// ns</span></div>
369
<div class="line"><a name="l00363"></a><span class="lineno"> 363</span> </div>
370
<div class="line"><a name="l00364"></a><span class="lineno"> 364</span> <span class="preprocessor">#endif // OPENMS_TRANSFORMATIONS_FEATUREFINDER_SUPERHIRN_LCELUTIONPEAK_H</span></div>
371
<div class="ttc" id="classOpenMS_1_1LCElutionPeak_html_acb7760252e63bf27414aeb15575b3b68"><div class="ttname"><a href="classOpenMS_1_1LCElutionPeak.html#acb7760252e63bf27414aeb15575b3b68">OpenMS::LCElutionPeak::DEBUG_MASS_END</a></div><div class="ttdeci">static double DEBUG_MASS_END</div><div class="ttdef"><b>Definition:</b> LCElutionPeak.h:110</div></div>
372
<div class="ttc" id="classOpenMS_1_1LCElutionPeak_html_a7c2cde6b2669674ee10ac27ed0b38f03"><div class="ttname"><a href="classOpenMS_1_1LCElutionPeak.html#a7c2cde6b2669674ee10ac27ed0b38f03">OpenMS::LCElutionPeak::update_CHRGMAP</a></div><div class="ttdeci">void update_CHRGMAP(MSPeak *IN)</div><div class="ttdef"><b>Definition:</b> LCElutionPeak.h:250</div></div>
373
<div class="ttc" id="classOpenMS_1_1LCElutionPeak_html_aa2f8a9c427c40f47910cdbfa03915cd8"><div class="ttname"><a href="classOpenMS_1_1LCElutionPeak.html#aa2f8a9c427c40f47910cdbfa03915cd8">OpenMS::LCElutionPeak::set_end_retention_time</a></div><div class="ttdeci">void set_end_retention_time(double IN)</div><div class="ttdef"><b>Definition:</b> LCElutionPeak.h:324</div></div>
374
<div class="ttc" id="classOpenMS_1_1LCElutionPeak_html_a47e3af93b063da2448711d8a8f250a1a"><div class="ttname"><a href="classOpenMS_1_1LCElutionPeak.html#a47e3af93b063da2448711d8a8f250a1a">OpenMS::LCElutionPeak::get_signal_list_end</a></div><div class="ttdeci">SIGNAL_iterator get_signal_list_end()</div><div class="ttdef"><b>Definition:</b> LCElutionPeak.h:233</div></div>
375
<div class="ttc" id="classOpenMS_1_1LCElutionPeak_html_a4bb41c31d39852daaa13eb35f5f04b23"><div class="ttname"><a href="classOpenMS_1_1LCElutionPeak.html#a4bb41c31d39852daaa13eb35f5f04b23">OpenMS::LCElutionPeak::getSignalToNoise</a></div><div class="ttdeci">double getSignalToNoise()</div><div class="ttdef"><b>Definition:</b> LCElutionPeak.h:350</div></div>
376
<div class="ttc" id="classOpenMS_1_1LCElutionPeak_html_aa35ecbe8a1c84b062addb6b6255b2fb2"><div class="ttname"><a href="classOpenMS_1_1LCElutionPeak.html#aa35ecbe8a1c84b062addb6b6255b2fb2">OpenMS::LCElutionPeak::fScanNumberApex</a></div><div class="ttdeci">int fScanNumberApex</div><div class="ttdef"><b>Definition:</b> LCElutionPeak.h:85</div></div>
377
<div class="ttc" id="classOpenMS_1_1LCElutionPeak_html_a068dc107c061c02358e286404d49258a"><div class="ttname"><a href="classOpenMS_1_1LCElutionPeak.html#a068dc107c061c02358e286404d49258a">OpenMS::LCElutionPeak::get_end_retention_time</a></div><div class="ttdeci">double get_end_retention_time()</div><div class="ttdef"><b>Definition:</b> LCElutionPeak.h:329</div></div>
378
<div class="ttc" id="classOpenMS_1_1LCElutionPeak_html_a02910972b1977ebde5a95e3b86d7722b"><div class="ttname"><a href="classOpenMS_1_1LCElutionPeak.html#a02910972b1977ebde5a95e3b86d7722b">OpenMS::LCElutionPeak::fpeak_area</a></div><div class="ttdeci">double fpeak_area</div><div class="ttdef"><b>Definition:</b> LCElutionPeak.h:91</div></div>
379
<div class="ttc" id="classOpenMS_1_1LCElutionPeak_html_a9161872721a7fda574c3e2133d69a9a9"><div class="ttname"><a href="classOpenMS_1_1LCElutionPeak.html#a9161872721a7fda574c3e2133d69a9a9">OpenMS::LCElutionPeak::getSignalToNoiseBackground</a></div><div class="ttdeci">double getSignalToNoiseBackground()</div><div class="ttdef"><b>Definition:</b> LCElutionPeak.h:355</div></div>
380
<div class="ttc" id="classOpenMS_1_1LCElutionPeak_html_a2e1ce7191795f93224d0c7c556dc54fa"><div class="ttname"><a href="classOpenMS_1_1LCElutionPeak.html#a2e1ce7191795f93224d0c7c556dc54fa">OpenMS::LCElutionPeak::fCharge</a></div><div class="ttdeci">int fCharge</div><div class="ttdef"><b>Definition:</b> LCElutionPeak.h:83</div></div>
381
<div class="ttc" id="classOpenMS_1_1LCElutionPeak_html_a6cf5b2361685fd6e7fde43a96498ce9e"><div class="ttname"><a href="classOpenMS_1_1LCElutionPeak.html#a6cf5b2361685fd6e7fde43a96498ce9e">OpenMS::LCElutionPeak::fScanNumberStart</a></div><div class="ttdeci">int fScanNumberStart</div><div class="ttdef"><b>Definition:</b> LCElutionPeak.h:84</div></div>
382
<div class="ttc" id="classOpenMS_1_1LCElutionPeak_html_a99157c03ee77754d15cb31611586265d"><div class="ttname"><a href="classOpenMS_1_1LCElutionPeak.html#a99157c03ee77754d15cb31611586265d">OpenMS::LCElutionPeak::fapex_intensity</a></div><div class="ttdeci">double fapex_intensity</div><div class="ttdef"><b>Definition:</b> LCElutionPeak.h:87</div></div>
383
<div class="ttc" id="classOpenMS_1_1LCElutionPeak_html_a00e30b5e53b81e2957fb095937eab517"><div class="ttname"><a href="classOpenMS_1_1LCElutionPeak.html#a00e30b5e53b81e2957fb095937eab517">OpenMS::LCElutionPeak::set_start_retention_time</a></div><div class="ttdeci">void set_start_retention_time(double IN)</div><div class="ttdef"><b>Definition:</b> LCElutionPeak.h:314</div></div>
384
<div class="ttc" id="classOpenMS_1_1LCElutionPeak_html_aedffea12c90a091f3642027871dcce00"><div class="ttname"><a href="classOpenMS_1_1LCElutionPeak.html#aedffea12c90a091f3642027871dcce00">OpenMS::LCElutionPeak::get_intensity</a></div><div class="ttdeci">float get_intensity(int IN)</div><div class="ttdef"><b>Definition:</b> LCElutionPeak.h:287</div></div>
385
<div class="ttc" id="classOpenMS_1_1LCElutionPeak_html_ac81d671afeef6f8fb49a01556d7ca47c"><div class="ttname"><a href="classOpenMS_1_1LCElutionPeak.html#ac81d671afeef6f8fb49a01556d7ca47c">OpenMS::LCElutionPeak::setElutionPeakExtraInfo</a></div><div class="ttdeci">void setElutionPeakExtraInfo(std::string in)</div><div class="ttdef"><b>Definition:</b> LCElutionPeak.h:211</div></div>
386
<div class="ttc" id="classOpenMS_1_1LCElutionPeak_html_a5bdcacef9b788e18c0dd8c323186c390"><div class="ttname"><a href="classOpenMS_1_1LCElutionPeak.html#a5bdcacef9b788e18c0dd8c323186c390">OpenMS::LCElutionPeak::get_start_scan</a></div><div class="ttdeci">int get_start_scan()</div><div class="ttdef"><b>Definition:</b> LCElutionPeak.h:304</div></div>
387
<div class="ttc" id="classOpenMS_1_1ConsensusIsotopePattern_html"><div class="ttname"><a href="classOpenMS_1_1ConsensusIsotopePattern.html">OpenMS::ConsensusIsotopePattern</a></div><div class="ttdef"><b>Definition:</b> ConsensusIsotopePattern.h:56</div></div>
388
<div class="ttc" id="classOpenMS_1_1LCElutionPeak_html_addc9ab666f80e876c8571db7f3a8e069"><div class="ttname"><a href="classOpenMS_1_1LCElutionPeak.html#addc9ab666f80e876c8571db7f3a8e069">OpenMS::LCElutionPeak::fSNIntensityThreshold</a></div><div class="ttdeci">double fSNIntensityThreshold</div><div class="ttdef"><b>Definition:</b> LCElutionPeak.h:93</div></div>
389
<div class="ttc" id="ConsensusIsotopePattern_8h_html"><div class="ttname"><a href="ConsensusIsotopePattern_8h.html">ConsensusIsotopePattern.h</a></div></div>
390
<div class="ttc" id="classOpenMS_1_1LCElutionPeak_html_a7cc0ff90acee6ff6f42056737fb78a22"><div class="ttname"><a href="classOpenMS_1_1LCElutionPeak.html#a7cc0ff90acee6ff6f42056737fb78a22">OpenMS::LCElutionPeak::get_charge_state</a></div><div class="ttdeci">int get_charge_state()</div><div class="ttdef"><b>Definition:</b> LCElutionPeak.h:343</div></div>
391
<div class="ttc" id="classOpenMS_1_1MSPeak_html_a56d6a680a88ac07ad6e23417cfbebb6f"><div class="ttname"><a href="classOpenMS_1_1MSPeak.html#a56d6a680a88ac07ad6e23417cfbebb6f">OpenMS::MSPeak::get_charge_state</a></div><div class="ttdeci">unsigned int get_charge_state()</div><div class="ttdef"><b>Definition:</b> MSPeak.h:221</div></div>
392
<div class="ttc" id="classOpenMS_1_1LCElutionPeak_html_aa34a1124f2a9332ea102d2cab19580c2"><div class="ttname"><a href="classOpenMS_1_1LCElutionPeak.html#aa34a1124f2a9332ea102d2cab19580c2">OpenMS::LCElutionPeak::CHRG_MAP</a></div><div class="ttdeci">std::multimap< int, int > CHRG_MAP</div><div class="ttdef"><b>Definition:</b> LCElutionPeak.h:101</div></div>
393
<div class="ttc" id="classOpenMS_1_1LCElutionPeak_html_ab3d9ebea3826de1e67b776e6579f9af1"><div class="ttname"><a href="classOpenMS_1_1LCElutionPeak.html#ab3d9ebea3826de1e67b776e6579f9af1">OpenMS::LCElutionPeak::get_apex_MZ</a></div><div class="ttdeci">double get_apex_MZ()</div><div class="ttdef"><b>Definition:</b> LCElutionPeak.h:280</div></div>
394
<div class="ttc" id="classOpenMS_1_1LCElutionPeak_html_aae48edd486239c935bb45c15712fa9e5"><div class="ttname"><a href="classOpenMS_1_1LCElutionPeak.html#aae48edd486239c935bb45c15712fa9e5">OpenMS::LCElutionPeak::elutionPeakExtraInfo</a></div><div class="ttdeci">std::string elutionPeakExtraInfo</div><div class="ttdef"><b>Definition:</b> LCElutionPeak.h:96</div></div>
395
<div class="ttc" id="classOpenMS_1_1LCElutionPeak_html_a49294cdec251db872fb2b9355a697057"><div class="ttname"><a href="classOpenMS_1_1LCElutionPeak.html#a49294cdec251db872fb2b9355a697057">OpenMS::LCElutionPeak::set_apex_retention_time</a></div><div class="ttdeci">void set_apex_retention_time(double IN)</div><div class="ttdef"><b>Definition:</b> LCElutionPeak.h:244</div></div>
396
<div class="ttc" id="classOpenMS_1_1LCElutionPeak_html_a44cd080df0f59602c14eb29fb6128cc5"><div class="ttname"><a href="classOpenMS_1_1LCElutionPeak.html#a44cd080df0f59602c14eb29fb6128cc5">OpenMS::LCElutionPeak::fRT</a></div><div class="ttdeci">double fRT</div><div class="ttdef"><b>Definition:</b> LCElutionPeak.h:88</div></div>
397
<div class="ttc" id="classOpenMS_1_1LCElutionPeak_html_abdecd7687dcc666c696fca36cb7ee768"><div class="ttname"><a href="classOpenMS_1_1LCElutionPeak.html#abdecd7687dcc666c696fca36cb7ee768">OpenMS::LCElutionPeak::intens_signals</a></div><div class="ttdeci">std::multimap< int, MSPeak > intens_signals</div><div class="ttdef"><b>Definition:</b> LCElutionPeak.h:99</div></div>
398
<div class="ttc" id="classOpenMS_1_1LCElutionPeak_html_a1e5411880247f3ff9aed8ed75b23b7e4"><div class="ttname"><a href="classOpenMS_1_1LCElutionPeak.html#a1e5411880247f3ff9aed8ed75b23b7e4">OpenMS::LCElutionPeak::get_start_retention_time</a></div><div class="ttdeci">double get_start_retention_time()</div><div class="ttdef"><b>Definition:</b> LCElutionPeak.h:319</div></div>
399
<div class="ttc" id="classOpenMS_1_1LCElutionPeak_html_a204b174e9a86216f70de4eb0aa71fda6"><div class="ttname"><a href="classOpenMS_1_1LCElutionPeak.html#a204b174e9a86216f70de4eb0aa71fda6">OpenMS::LCElutionPeak::fEndTR</a></div><div class="ttdeci">double fEndTR</div><div class="ttdef"><b>Definition:</b> LCElutionPeak.h:90</div></div>
400
<div class="ttc" id="classOpenMS_1_1LCElutionPeak_html_a71bd48a0a57a43a9d57adb02cf478e47"><div class="ttname"><a href="classOpenMS_1_1LCElutionPeak.html#a71bd48a0a57a43a9d57adb02cf478e47">OpenMS::LCElutionPeak::get_apex_retention_time</a></div><div class="ttdeci">double get_apex_retention_time()</div><div class="ttdef"><b>Definition:</b> LCElutionPeak.h:275</div></div>
401
<div class="ttc" id="classOpenMS_1_1LCElutionPeak_html_ab812559cf209574e7cdc97e740d8600e"><div class="ttname"><a href="classOpenMS_1_1LCElutionPeak.html#ab812559cf209574e7cdc97e740d8600e">OpenMS::LCElutionPeak::get_apex_intensity</a></div><div class="ttdeci">double get_apex_intensity()</div><div class="ttdef"><b>Definition:</b> LCElutionPeak.h:270</div></div>
402
<div class="ttc" id="classOpenMS_1_1MSPeak_html"><div class="ttname"><a href="classOpenMS_1_1MSPeak.html">OpenMS::MSPeak</a></div><div class="ttdef"><b>Definition:</b> MSPeak.h:64</div></div>
403
<div class="ttc" id="classOpenMS_1_1LCElutionPeak_html_aaab6cb4b26d8f84a94eee092b755c66b"><div class="ttname"><a href="classOpenMS_1_1LCElutionPeak.html#aaab6cb4b26d8f84a94eee092b755c66b">OpenMS::LCElutionPeak::get_signal_list_start</a></div><div class="ttdeci">SIGNAL_iterator get_signal_list_start()</div><div class="ttdef"><b>Definition:</b> LCElutionPeak.h:228</div></div>
404
<div class="ttc" id="classOpenMS_1_1LCElutionPeak_html_aeacd03494bac7bbad33feadfb81e613a"><div class="ttname"><a href="classOpenMS_1_1LCElutionPeak.html#aeacd03494bac7bbad33feadfb81e613a">OpenMS::LCElutionPeak::DEBUG_MASS_START</a></div><div class="ttdeci">static double DEBUG_MASS_START</div><div class="ttdef"><b>Definition:</b> LCElutionPeak.h:109</div></div>
405
<div class="ttc" id="classOpenMS_1_1LCElutionPeak_html_a0f4a36df4dbdfd4a99366bcd24ae344f"><div class="ttname"><a href="classOpenMS_1_1LCElutionPeak.html#a0f4a36df4dbdfd4a99366bcd24ae344f">OpenMS::LCElutionPeak::get_total_peak_area</a></div><div class="ttdeci">double get_total_peak_area()</div><div class="ttdef"><b>Definition:</b> LCElutionPeak.h:297</div></div>
406
<div class="ttc" id="namespaceOpenMS_html_ab69ab1a8bcf64e4e36a57672502f93dc"><div class="ttname"><a href="namespaceOpenMS.html#ab69ab1a8bcf64e4e36a57672502f93dc">OpenMS::MZ_series</a></div><div class="ttdeci">std::vector< elution_peak > MZ_series</div><div class="ttdef"><b>Definition:</b> LCElutionPeak.h:61</div></div>
407
<div class="ttc" id="classOpenMS_1_1LCElutionPeak_html_a3e554fdf19c9a25b10ec1264bf68bec8"><div class="ttname"><a href="classOpenMS_1_1LCElutionPeak.html#a3e554fdf19c9a25b10ec1264bf68bec8">OpenMS::LCElutionPeak::f_observed_Mass</a></div><div class="ttdeci">double f_observed_Mass</div><div class="ttdef"><b>Definition:</b> LCElutionPeak.h:76</div></div>
408
<div class="ttc" id="classOpenMS_1_1LCElutionPeak_html_ac51a16752e2e401cad22b5f6c2665924"><div class="ttname"><a href="classOpenMS_1_1LCElutionPeak.html#ac51a16752e2e401cad22b5f6c2665924">OpenMS::LCElutionPeak::fMonoMass</a></div><div class="ttdeci">double fMonoMass</div><div class="ttdef"><b>Definition:</b> LCElutionPeak.h:81</div></div>
409
<div class="ttc" id="classOpenMS_1_1LCElutionPeak_html_a364c5a3b05ab685c42af06bc462b3344"><div class="ttname"><a href="classOpenMS_1_1LCElutionPeak.html#a364c5a3b05ab685c42af06bc462b3344">OpenMS::LCElutionPeak::getElutionPeakExtraInfo</a></div><div class="ttdeci">std::string getElutionPeakExtraInfo()</div><div class="ttdef"><b>Definition:</b> LCElutionPeak.h:216</div></div>
410
<div class="ttc" id="classOpenMS_1_1LCElutionPeak_html_a721772ba0ec677852bf5c94ae467c195"><div class="ttname"><a href="classOpenMS_1_1LCElutionPeak.html#a721772ba0ec677852bf5c94ae467c195">OpenMS::LCElutionPeak::APEX</a></div><div class="ttdeci">MSPeak * APEX</div><div class="ttdef"><b>Definition:</b> LCElutionPeak.h:94</div></div>
411
<div class="ttc" id="classOpenMS_1_1LCElutionPeak_html_a64013730f99f52c28ff480e63b75ea78"><div class="ttname"><a href="classOpenMS_1_1LCElutionPeak.html#a64013730f99f52c28ff480e63b75ea78">OpenMS::LCElutionPeak::fSignalToNoise</a></div><div class="ttdeci">double fSignalToNoise</div><div class="ttdef"><b>Definition:</b> LCElutionPeak.h:92</div></div>
412
<div class="ttc" id="classOpenMS_1_1LCElutionPeak_html_aa624be0a99fd8e5e73fc019d3f5790e1"><div class="ttname"><a href="classOpenMS_1_1LCElutionPeak.html#aa624be0a99fd8e5e73fc019d3f5790e1">OpenMS::LCElutionPeak::isotopePattern</a></div><div class="ttdeci">ConsensusIsotopePattern * isotopePattern</div><div class="ttdef"><b>Definition:</b> LCElutionPeak.h:74</div></div>
413
<div class="ttc" id="classOpenMS_1_1LCElutionPeak_html_ae08b9afa83396a99cf29848c902b1b5f"><div class="ttname"><a href="classOpenMS_1_1LCElutionPeak.html#ae08b9afa83396a99cf29848c902b1b5f">OpenMS::LCElutionPeak::fNrIsotopes</a></div><div class="ttdeci">int fNrIsotopes</div><div class="ttdef"><b>Definition:</b> LCElutionPeak.h:75</div></div>
414
<div class="ttc" id="classOpenMS_1_1LCElutionPeak_html_a1a0d8a914f8b9c1189829edcb142a93d"><div class="ttname"><a href="classOpenMS_1_1LCElutionPeak.html#a1a0d8a914f8b9c1189829edcb142a93d">OpenMS::LCElutionPeak::get_scan_apex</a></div><div class="ttdeci">int get_scan_apex()</div><div class="ttdef"><b>Definition:</b> LCElutionPeak.h:265</div></div>
415
<div class="ttc" id="classOpenMS_1_1LCElutionPeak_html_af77af24ac504f5f44a91f1ca24f34864"><div class="ttname"><a href="classOpenMS_1_1LCElutionPeak.html#af77af24ac504f5f44a91f1ca24f34864">OpenMS::LCElutionPeak::fScanNumberEnd</a></div><div class="ttdeci">int fScanNumberEnd</div><div class="ttdef"><b>Definition:</b> LCElutionPeak.h:86</div></div>
416
<div class="ttc" id="classOpenMS_1_1LCElutionPeak_html_a7a3ac2f5ce9bd348d2fde4597d7c8bed"><div class="ttname"><a href="classOpenMS_1_1LCElutionPeak.html#a7a3ac2f5ce9bd348d2fde4597d7c8bed">OpenMS::LCElutionPeak::fVolume</a></div><div class="ttdeci">double fVolume</div><div class="ttdef"><b>Definition:</b> LCElutionPeak.h:82</div></div>
417
<div class="ttc" id="classOpenMS_1_1LCElutionPeak_html_a53ac877069cd954216c872fa56d301db"><div class="ttname"><a href="classOpenMS_1_1LCElutionPeak.html#a53ac877069cd954216c872fa56d301db">OpenMS::LCElutionPeak::get_nb_ms_peaks</a></div><div class="ttdeci">int get_nb_ms_peaks()</div><div class="ttdef"><b>Definition:</b> LCElutionPeak.h:336</div></div>
418
<div class="ttc" id="classOpenMS_1_1LCElutionPeak_html"><div class="ttname"><a href="classOpenMS_1_1LCElutionPeak.html">OpenMS::LCElutionPeak</a></div><div class="ttdef"><b>Definition:</b> LCElutionPeak.h:65</div></div>
419
<div class="ttc" id="classOpenMS_1_1LCElutionPeak_html_a6fec4c9e10aa7806d2e811e5f59f2219"><div class="ttname"><a href="classOpenMS_1_1LCElutionPeak.html#a6fec4c9e10aa7806d2e811e5f59f2219">OpenMS::LCElutionPeak::analyzeLCElutionPeak</a></div><div class="ttdeci">void analyzeLCElutionPeak()</div><div class="ttdef"><b>Definition:</b> LCElutionPeak.h:133</div></div>
420
<div class="ttc" id="classOpenMS_1_1LCElutionPeak_html_a508b1c44a0cfd87efba4d6a2febb4231"><div class="ttname"><a href="classOpenMS_1_1LCElutionPeak.html#a508b1c44a0cfd87efba4d6a2febb4231">OpenMS::LCElutionPeak::fIsotopMass</a></div><div class="ttdeci">double fIsotopMass</div><div class="ttdef"><b>Definition:</b> LCElutionPeak.h:77</div></div>
421
<div class="ttc" id="classOpenMS_1_1LCElutionPeak_html_a312f7c201776e27ecd97e85a0e7f5024"><div class="ttname"><a href="classOpenMS_1_1LCElutionPeak.html#a312f7c201776e27ecd97e85a0e7f5024">OpenMS::LCElutionPeak::fStartTR</a></div><div class="ttdeci">double fStartTR</div><div class="ttdef"><b>Definition:</b> LCElutionPeak.h:89</div></div>
422
<div class="ttc" id="namespaceOpenMS_html_a79e6b2973636a97ad0228a737ddcbed6"><div class="ttname"><a href="namespaceOpenMS.html#a79e6b2973636a97ad0228a737ddcbed6">OpenMS::MZ_series_ITERATOR</a></div><div class="ttdeci">std::vector< elution_peak >::iterator MZ_series_ITERATOR</div><div class="ttdef"><b>Definition:</b> LCElutionPeak.h:62</div></div>
423
<div class="ttc" id="classOpenMS_1_1LCElutionPeak_html_aa5d97ba2d1f5db95c28860a4a2c5ce36"><div class="ttname"><a href="classOpenMS_1_1LCElutionPeak.html#aa5d97ba2d1f5db95c28860a4a2c5ce36">OpenMS::LCElutionPeak::get_end_scan</a></div><div class="ttdeci">int get_end_scan()</div><div class="ttdef"><b>Definition:</b> LCElutionPeak.h:309</div></div>
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<div class="ttc" id="namespaceOpenMS_html_a86f33425d6d3c820cf964cacc9a3fd34"><div class="ttname"><a href="namespaceOpenMS.html#a86f33425d6d3c820cf964cacc9a3fd34">OpenMS::SIGNAL_iterator</a></div><div class="ttdeci">std::multimap< int, MSPeak >::iterator SIGNAL_iterator</div><div class="ttdef"><b>Definition:</b> LCElutionPeak.h:63</div></div>
425
<div class="ttc" id="namespaceOpenMS_html_af18558f60329d153e5f439e6b6cbc6fa"><div class="ttname"><a href="namespaceOpenMS.html#af18558f60329d153e5f439e6b6cbc6fa">OpenMS::elution_peak</a></div><div class="ttdeci">std::multimap< int, MSPeak > elution_peak</div><div class="ttdef"><b>Definition:</b> LCElutionPeak.h:60</div></div>
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<HR style="height:1px; border:none; border-top:1px solid #c0c0c0;">
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<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
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<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:16 using doxygen 1.8.5</font></TD>
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