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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_cf999e13dd2b4cfaf0739996c075e697.html">FILTERING</a></li><li class="navelem"><a class="el" href="dir_1a81ea060069865671a52f0bbef0e7ac.html">DATAREDUCTION</a></li> </ul>
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<div class="title">SILACFilter.h</div> </div>
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27
<a href="SILACFilter_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>
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<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: Lars Nilse $</span></div>
58
<div class="line"><a name="l00032"></a><span class="lineno"> 32</span> <span class="comment">// $Authors: Steffen Sass, Holger Plattfaut, Bastian Blank $</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> </div>
61
<div class="line"><a name="l00035"></a><span class="lineno"> 35</span> <span class="preprocessor">#ifndef OPENMS_FILTERING_DATAREDUCTION_SILACFILTER_H</span></div>
62
<div class="line"><a name="l00036"></a><span class="lineno"> 36</span> <span class="preprocessor"></span><span class="preprocessor">#define OPENMS_FILTERING_DATAREDUCTION_SILACFILTER_H</span></div>
63
<div class="line"><a name="l00037"></a><span class="lineno"> 37</span> <span class="preprocessor"></span></div>
64
<div class="line"><a name="l00038"></a><span class="lineno"> 38</span> <span class="preprocessor">#include <<a class="code" href="StandardTypes_8h.html">OpenMS/KERNEL/StandardTypes.h</a>></span></div>
65
<div class="line"><a name="l00039"></a><span class="lineno"> 39</span> <span class="preprocessor">#include <<a class="code" href="SILACFiltering_8h.html">OpenMS/FILTERING/DATAREDUCTION/SILACFiltering.h</a>></span></div>
66
<div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="preprocessor">#include <<a class="code" href="SILACPattern_8h.html">OpenMS/FILTERING/DATAREDUCTION/SILACPattern.h</a>></span></div>
67
<div class="line"><a name="l00041"></a><span class="lineno"> 41</span> <span class="preprocessor">#include <<a class="code" href="IsotopeDistributionCache_8h.html">OpenMS/FILTERING/DATAREDUCTION/IsotopeDistributionCache.h</a>></span></div>
68
<div class="line"><a name="l00042"></a><span class="lineno"> 42</span> <span class="preprocessor">#include <gsl/gsl_interp.h></span></div>
69
<div class="line"><a name="l00043"></a><span class="lineno"> 43</span> <span class="preprocessor">#include <gsl/gsl_spline.h></span></div>
70
<div class="line"><a name="l00044"></a><span class="lineno"> 44</span> <span class="preprocessor">#include <queue></span></div>
71
<div class="line"><a name="l00045"></a><span class="lineno"> 45</span> <span class="preprocessor">#include <list></span></div>
72
<div class="line"><a name="l00046"></a><span class="lineno"> 46</span> </div>
73
<div class="line"><a name="l00047"></a><span class="lineno"> 47</span> <span class="keyword">namespace </span>OpenMS</div>
74
<div class="line"><a name="l00048"></a><span class="lineno"> 48</span> {</div>
75
<div class="line"><a name="l00058"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SILACFilter.html"> 58</a></span>  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1SILACFilter.html">SILACFilter</a></div>
76
<div class="line"><a name="l00059"></a><span class="lineno"> 59</span>  {</div>
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<div class="line"><a name="l00060"></a><span class="lineno"> 60</span> <span class="keyword">private</span>:</div>
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<div class="line"><a name="l00061"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SILACFilter.html#a232a35ac3c539a5963d1ce03891038db"> 61</a></span>  <span class="keyword">friend</span> <span class="keyword">class </span><a class="code" href="classOpenMS_1_1SILACFiltering.html">SILACFiltering</a>;</div>
79
<div class="line"><a name="l00062"></a><span class="lineno"> 62</span> </div>
80
<div class="line"><a name="l00063"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SILACFilter.html#a13ba56ed55f3af6673f1f8799f2302bb"> 63</a></span>  <span class="keyword">typedef</span> <a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1TheoreticalIsotopePattern.html">IsotopeDistributionCache::TheoreticalIsotopePattern</a> <a class="code" href="classOpenMS_1_1SILACFilter.html#a13ba56ed55f3af6673f1f8799f2302bb">TheoreticalIsotopePattern</a>;</div>
81
<div class="line"><a name="l00064"></a><span class="lineno"> 64</span> </div>
82
<div class="line"><a name="l00068"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SILACFilter.html#a2aa63bc126ed23ea610a514c86c6e520"> 68</a></span>  std::vector<DoubleReal> <a class="code" href="classOpenMS_1_1SILACFilter.html#a2aa63bc126ed23ea610a514c86c6e520">mass_separations_</a>;</div>
83
<div class="line"><a name="l00069"></a><span class="lineno"> 69</span> </div>
84
<div class="line"><a name="l00073"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SILACFilter.html#af71274961d8487036283991f2ba652a1"> 73</a></span>  <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> <a class="code" href="classOpenMS_1_1SILACFilter.html#af71274961d8487036283991f2ba652a1">charge_</a>;</div>
85
<div class="line"><a name="l00074"></a><span class="lineno"> 74</span> </div>
86
<div class="line"><a name="l00078"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SILACFilter.html#a0d2ee74c56a3e7eaa73e7d0591d7caef"> 78</a></span>  <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1SILACFilter.html#a0d2ee74c56a3e7eaa73e7d0591d7caef">model_deviation_</a>;</div>
87
<div class="line"><a name="l00079"></a><span class="lineno"> 79</span> </div>
88
<div class="line"><a name="l00083"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SILACFilter.html#a8377d39af6229a0742191116468bb9f5"> 83</a></span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="classOpenMS_1_1SILACFilter.html#a8377d39af6229a0742191116468bb9f5">isotopes_per_peptide_</a>;</div>
89
<div class="line"><a name="l00084"></a><span class="lineno"> 84</span> </div>
90
<div class="line"><a name="l00088"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SILACFilter.html#a130cafea98e2066ba4cc66a7b6812485"> 88</a></span>  <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1SILACFilter.html#a130cafea98e2066ba4cc66a7b6812485">intensity_cutoff_</a>;</div>
91
<div class="line"><a name="l00089"></a><span class="lineno"> 89</span> </div>
92
<div class="line"><a name="l00093"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SILACFilter.html#ac82a29983c547ce48303395ccd6362d0"> 93</a></span>  <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1SILACFilter.html#ac82a29983c547ce48303395ccd6362d0">intensity_correlation_</a>;</div>
93
<div class="line"><a name="l00094"></a><span class="lineno"> 94</span> </div>
94
<div class="line"><a name="l00098"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SILACFilter.html#a661ca7fc27d997f31cb2f5043a25571f"> 98</a></span>  <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1SILACFilter.html#a661ca7fc27d997f31cb2f5043a25571f">allow_missing_peaks_</a>;</div>
95
<div class="line"><a name="l00099"></a><span class="lineno"> 99</span> </div>
96
<div class="line"><a name="l00103"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SILACFilter.html#ad10cc346f44534120f62ea1d76f279b2"> 103</a></span>  <span class="keyword">static</span> <a class="code" href="classOpenMS_1_1IsotopeDistributionCache.html">IsotopeDistributionCache</a> * <a class="code" href="classOpenMS_1_1SILACFilter.html#ad10cc346f44534120f62ea1d76f279b2">isotope_distribution_</a>;</div>
97
<div class="line"><a name="l00104"></a><span class="lineno"> 104</span> </div>
98
<div class="line"><a name="l00108"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SILACFilter.html#a77a4124bcddddbacc0cb5a08a8204211"> 108</a></span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="classOpenMS_1_1SILACFilter.html#a77a4124bcddddbacc0cb5a08a8204211">number_of_peptides_</a>;</div>
99
<div class="line"><a name="l00109"></a><span class="lineno"> 109</span> </div>
100
<div class="line"><a name="l00113"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SILACFilter.html#af1b731c7f8e6095c30ed0b7148eaf16e"> 113</a></span>  std::vector<DoubleReal> <a class="code" href="classOpenMS_1_1SILACFilter.html#af1b731c7f8e6095c30ed0b7148eaf16e">peak_positions_</a>;</div>
101
<div class="line"><a name="l00114"></a><span class="lineno"> 114</span> </div>
102
<div class="line"><a name="l00118"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SILACFilter.html#af1be142aa6415d3b1a5cc6f961ceaa41"> 118</a></span>  std::vector<DoubleReal> <a class="code" href="classOpenMS_1_1SILACFilter.html#af1be142aa6415d3b1a5cc6f961ceaa41">mz_peptide_separations_</a>;</div>
103
<div class="line"><a name="l00119"></a><span class="lineno"> 119</span> </div>
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<div class="line"><a name="l00123"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SILACFilter.html#a2137970416910409891f9a50c918630d"> 123</a></span>  std::vector<DoubleReal> <a class="code" href="classOpenMS_1_1SILACFilter.html#a2137970416910409891f9a50c918630d">expected_mz_shifts_</a>;</div>
105
<div class="line"><a name="l00124"></a><span class="lineno"> 124</span> </div>
106
<div class="line"><a name="l00128"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SILACFilter.html#a7712c402061a69ebf5904810f8b27d12"> 128</a></span>  <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1SILACFilter.html#a7712c402061a69ebf5904810f8b27d12">isotope_distance_</a>;</div>
107
<div class="line"><a name="l00129"></a><span class="lineno"> 129</span> </div>
108
<div class="line"><a name="l00133"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SILACFilter.html#ac6bad96f1ef902eafcbd7471bfced374"> 133</a></span>  std::vector<SILACPattern> <a class="code" href="classOpenMS_1_1SILACFilter.html#ac6bad96f1ef902eafcbd7471bfced374">elements_</a>;</div>
109
<div class="line"><a name="l00134"></a><span class="lineno"> 134</span> </div>
110
<div class="line"><a name="l00138"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SILACFilter.html#a8ab5115f2ddcdd7a96ca0186716af877"> 138</a></span>  <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1SILACFilter.html#a8ab5115f2ddcdd7a96ca0186716af877">current_mz_</a>;</div>
111
<div class="line"><a name="l00139"></a><span class="lineno"> 139</span> </div>
112
<div class="line"><a name="l00143"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SILACFilter.html#a8ff1090fdf921b85d9440aac2903e805"> 143</a></span>  std::vector<std::vector<DoubleReal> > <a class="code" href="classOpenMS_1_1SILACFilter.html#a8ff1090fdf921b85d9440aac2903e805">exact_shifts_</a>;</div>
113
<div class="line"><a name="l00144"></a><span class="lineno"> 144</span> </div>
114
<div class="line"><a name="l00148"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SILACFilter.html#af87dc576f79e04d5c793759410bb32f0"> 148</a></span>  std::vector<std::vector<DoubleReal> > <a class="code" href="classOpenMS_1_1SILACFilter.html#af87dc576f79e04d5c793759410bb32f0">exact_mz_positions_</a>;</div>
115
<div class="line"><a name="l00149"></a><span class="lineno"> 149</span> </div>
116
<div class="line"><a name="l00153"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SILACFilter.html#a15861ea59b6250c5078ff42021d25d5a"> 153</a></span>  std::vector<std::vector<DoubleReal> > <a class="code" href="classOpenMS_1_1SILACFilter.html#a15861ea59b6250c5078ff42021d25d5a">exact_intensities_</a>;</div>
117
<div class="line"><a name="l00154"></a><span class="lineno"> 154</span> </div>
118
<div class="line"><a name="l00158"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SILACFilter.html#ab3412d59616219275e3e08165981e169"> 158</a></span>  std::vector<std::vector<DoubleReal> > <a class="code" href="classOpenMS_1_1SILACFilter.html#ab3412d59616219275e3e08165981e169">expected_shifts_</a>;</div>
119
<div class="line"><a name="l00159"></a><span class="lineno"> 159</span> </div>
120
<div class="line"><a name="l00165"></a><span class="lineno"> 165</span>  <span class="keywordtype">bool</span> isSILACPattern_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum<Peak1D></a> &, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1SILACFiltering_1_1SpectrumInterpolation.html">SILACFiltering::SpectrumInterpolation</a> &, <a class="code" href="classdouble.html">DoubleReal</a> mz, <a class="code" href="classdouble.html">DoubleReal</a> picked_mz, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1SILACFiltering.html">SILACFiltering</a> &, <a class="code" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum<Peak1D></a> & debug, <a class="code" href="classOpenMS_1_1SILACPattern.html">SILACPattern</a> & pattern);</div>
121
<div class="line"><a name="l00166"></a><span class="lineno"> 166</span> </div>
122
<div class="line"><a name="l00170"></a><span class="lineno"> 170</span>  <span class="keywordtype">bool</span> isSILACPatternPicked_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum<Peak1D></a> &, <a class="code" href="classdouble.html">DoubleReal</a> mz, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1SILACFiltering.html">SILACFiltering</a> &, <a class="code" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum<Peak1D></a> & debug);</div>
123
<div class="line"><a name="l00171"></a><span class="lineno"> 171</span> </div>
124
<div class="line"><a name="l00175"></a><span class="lineno"> 175</span>  <span class="keywordtype">bool</span> extractMzShiftsAndIntensities_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum<Peak1D></a> &, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1SILACFiltering_1_1SpectrumInterpolation.html">SILACFiltering::SpectrumInterpolation</a> &, <a class="code" href="classdouble.html">DoubleReal</a> mz, <a class="code" href="classdouble.html">DoubleReal</a> picked_mz, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1SILACFiltering.html">SILACFiltering</a> &);</div>
125
<div class="line"><a name="l00176"></a><span class="lineno"> 176</span> </div>
126
<div class="line"><a name="l00180"></a><span class="lineno"> 180</span>  <span class="keywordtype">bool</span> extractMzShiftsAndIntensitiesPicked_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum<Peak1D></a> &, <a class="code" href="classdouble.html">DoubleReal</a> mz, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1SILACFiltering.html">SILACFiltering</a> &);</div>
127
<div class="line"><a name="l00181"></a><span class="lineno"> 181</span> </div>
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<div class="line"><a name="l00185"></a><span class="lineno"> 185</span>  <span class="keywordtype">bool</span> extractMzShiftsAndIntensitiesPickedToPattern_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum<Peak1D></a> &, <a class="code" href="classdouble.html">DoubleReal</a> mz, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1SILACFiltering.html">SILACFiltering</a> &, <a class="code" href="classOpenMS_1_1SILACPattern.html">SILACPattern</a> & pattern);</div>
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<div class="line"><a name="l00186"></a><span class="lineno"> 186</span> </div>
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<div class="line"><a name="l00190"></a><span class="lineno"> 190</span>  <span class="keywordtype">bool</span> intensityFilter_();</div>
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<div class="line"><a name="l00191"></a><span class="lineno"> 191</span> </div>
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<div class="line"><a name="l00195"></a><span class="lineno"> 195</span>  <span class="keywordtype">bool</span> correlationFilter1_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1SILACFiltering_1_1SpectrumInterpolation.html">SILACFiltering::SpectrumInterpolation</a> &, <a class="code" href="classdouble.html">DoubleReal</a> mz, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1SILACFiltering.html">SILACFiltering</a> &);</div>
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<div class="line"><a name="l00196"></a><span class="lineno"> 196</span> </div>
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<div class="line"><a name="l00200"></a><span class="lineno"> 200</span>  <span class="keywordtype">bool</span> correlationFilter2_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1SILACFiltering_1_1SpectrumInterpolation.html">SILACFiltering::SpectrumInterpolation</a> &, <a class="code" href="classdouble.html">DoubleReal</a> mz, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1SILACFiltering.html">SILACFiltering</a> &);</div>
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<div class="line"><a name="l00201"></a><span class="lineno"> 201</span> </div>
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<div class="line"><a name="l00205"></a><span class="lineno"> 205</span>  <span class="keywordtype">bool</span> averageneFilter_(<a class="code" href="classdouble.html">DoubleReal</a> mz);</div>
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<div class="line"><a name="l00206"></a><span class="lineno"> 206</span> </div>
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<div class="line"><a name="l00207"></a><span class="lineno"> 207</span> <span class="keyword">public</span>:</div>
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<div class="line"><a name="l00218"></a><span class="lineno"> 218</span>  <a class="code" href="classOpenMS_1_1SILACFilter.html">SILACFilter</a>(std::vector<DoubleReal> mass_separations, <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> charge, <a class="code" href="classdouble.html">DoubleReal</a> model_deviation, <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> isotopes_per_peptide,</div>
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<div class="line"><a name="l00219"></a><span class="lineno"> 219</span>  <a class="code" href="classdouble.html">DoubleReal</a> intensity_cutoff, <a class="code" href="classdouble.html">DoubleReal</a> intensity_correlation, <span class="keywordtype">bool</span> allow_missing_peaks);</div>
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<div class="line"><a name="l00220"></a><span class="lineno"> 220</span> </div>
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<div class="line"><a name="l00224"></a><span class="lineno"> 224</span>  std::vector<DoubleReal> getPeakPositions();</div>
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<div class="line"><a name="l00225"></a><span class="lineno"> 225</span> </div>
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<div class="line"><a name="l00229"></a><span class="lineno"> 229</span>  <span class="keyword">const</span> std::vector<DoubleReal> & getExpectedMzShifts();</div>
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<div class="line"><a name="l00230"></a><span class="lineno"> 230</span> </div>
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<div class="line"><a name="l00234"></a><span class="lineno"> 234</span>  std::vector<SILACPattern> & getElements();</div>
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<div class="line"><a name="l00235"></a><span class="lineno"> 235</span> </div>
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<div class="line"><a name="l00239"></a><span class="lineno"> 239</span>  <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> getCharge();</div>
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<div class="line"><a name="l00240"></a><span class="lineno"> 240</span> </div>
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<div class="line"><a name="l00244"></a><span class="lineno"> 244</span>  std::vector<DoubleReal> & getMassSeparations();</div>
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<div class="line"><a name="l00245"></a><span class="lineno"> 245</span>  };</div>
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<div class="line"><a name="l00246"></a><span class="lineno"> 246</span> }</div>
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<div class="line"><a name="l00247"></a><span class="lineno"> 247</span> </div>
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<div class="line"><a name="l00248"></a><span class="lineno"> 248</span> <span class="preprocessor">#endif </span><span class="comment">/* SILACFILTER_H_ */</span><span class="preprocessor"></span></div>
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<div class="ttc" id="IsotopeDistributionCache_8h_html"><div class="ttname"><a href="IsotopeDistributionCache_8h.html">IsotopeDistributionCache.h</a></div></div>
156
<div class="ttc" id="classOpenMS_1_1SILACFilter_html_a8377d39af6229a0742191116468bb9f5"><div class="ttname"><a href="classOpenMS_1_1SILACFilter.html#a8377d39af6229a0742191116468bb9f5">OpenMS::SILACFilter::isotopes_per_peptide_</a></div><div class="ttdeci">Size isotopes_per_peptide_</div><div class="ttdoc">number of peaks per peptide to search for </div><div class="ttdef"><b>Definition:</b> SILACFilter.h:83</div></div>
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<div class="ttc" id="StandardTypes_8h_html"><div class="ttname"><a href="StandardTypes_8h.html">StandardTypes.h</a></div></div>
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<div class="ttc" id="classOpenMS_1_1SILACFilter_html_a0d2ee74c56a3e7eaa73e7d0591d7caef"><div class="ttname"><a href="classOpenMS_1_1SILACFilter.html#a0d2ee74c56a3e7eaa73e7d0591d7caef">OpenMS::SILACFilter::model_deviation_</a></div><div class="ttdeci">DoubleReal model_deviation_</div><div class="ttdoc">maximal value of which a predicted SILAC feature may deviate from the averagine model ...</div><div class="ttdef"><b>Definition:</b> SILACFilter.h:78</div></div>
159
<div class="ttc" id="classOpenMS_1_1SILACFilter_html_ad10cc346f44534120f62ea1d76f279b2"><div class="ttname"><a href="classOpenMS_1_1SILACFilter.html#ad10cc346f44534120f62ea1d76f279b2">OpenMS::SILACFilter::isotope_distribution_</a></div><div class="ttdeci">static IsotopeDistributionCache * isotope_distribution_</div><div class="ttdef"><b>Definition:</b> SILACFilter.h:103</div></div>
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<div class="ttc" id="classOpenMS_1_1SILACFilter_html_a8ff1090fdf921b85d9440aac2903e805"><div class="ttname"><a href="classOpenMS_1_1SILACFilter.html#a8ff1090fdf921b85d9440aac2903e805">OpenMS::SILACFilter::exact_shifts_</a></div><div class="ttdeci">std::vector< std::vector< DoubleReal > > exact_shifts_</div><div class="ttdoc">exact m/z shift of isotopic peaks in a SILAC pattern relative to the mono-isotopic peak of the light ...</div><div class="ttdef"><b>Definition:</b> SILACFilter.h:143</div></div>
161
<div class="ttc" id="classOpenMS_1_1SILACFilter_html_a130cafea98e2066ba4cc66a7b6812485"><div class="ttname"><a href="classOpenMS_1_1SILACFilter.html#a130cafea98e2066ba4cc66a7b6812485">OpenMS::SILACFilter::intensity_cutoff_</a></div><div class="ttdeci">DoubleReal intensity_cutoff_</div><div class="ttdoc">minimal intensity of SILAC features </div><div class="ttdef"><b>Definition:</b> SILACFilter.h:88</div></div>
162
<div class="ttc" id="classOpenMS_1_1SILACFilter_html_a7712c402061a69ebf5904810f8b27d12"><div class="ttname"><a href="classOpenMS_1_1SILACFilter.html#a7712c402061a69ebf5904810f8b27d12">OpenMS::SILACFilter::isotope_distance_</a></div><div class="ttdeci">DoubleReal isotope_distance_</div><div class="ttdoc">distance between isotopic peaks of a peptide in [Th] </div><div class="ttdef"><b>Definition:</b> SILACFilter.h:128</div></div>
163
<div class="ttc" id="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1TheoreticalIsotopePattern_html"><div class="ttname"><a href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1TheoreticalIsotopePattern.html">OpenMS::FeatureFinderAlgorithmPickedHelperStructs::TheoreticalIsotopePattern</a></div><div class="ttdoc">Helper structure for a theoretical isotope pattern used in FeatureFinderAlgorithmPicked. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPickedHelperStructs.h:277</div></div>
164
<div class="ttc" id="classOpenMS_1_1SILACFilter_html"><div class="ttname"><a href="classOpenMS_1_1SILACFilter.html">OpenMS::SILACFilter</a></div><div class="ttdoc">Filter to use for SILACFiltering. </div><div class="ttdef"><b>Definition:</b> SILACFilter.h:58</div></div>
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<div class="ttc" id="classdouble_html"><div class="ttname"><a href="classdouble.html">double</a></div></div>
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<div class="ttc" id="classOpenMS_1_1SILACFilter_html_a661ca7fc27d997f31cb2f5043a25571f"><div class="ttname"><a href="classOpenMS_1_1SILACFilter.html#a661ca7fc27d997f31cb2f5043a25571f">OpenMS::SILACFilter::allow_missing_peaks_</a></div><div class="ttdeci">bool allow_missing_peaks_</div><div class="ttdoc">flag for missing peaks </div><div class="ttdef"><b>Definition:</b> SILACFilter.h:98</div></div>
167
<div class="ttc" id="SILACFiltering_8h_html"><div class="ttname"><a href="SILACFiltering_8h.html">SILACFiltering.h</a></div></div>
168
<div class="ttc" id="classOpenMS_1_1MSSpectrum_html"><div class="ttname"><a href="classOpenMS_1_1MSSpectrum.html">OpenMS::MSSpectrum< Peak1D ></a></div></div>
169
<div class="ttc" id="classOpenMS_1_1SILACFilter_html_a2aa63bc126ed23ea610a514c86c6e520"><div class="ttname"><a href="classOpenMS_1_1SILACFilter.html#a2aa63bc126ed23ea610a514c86c6e520">OpenMS::SILACFilter::mass_separations_</a></div><div class="ttdeci">std::vector< DoubleReal > mass_separations_</div><div class="ttdoc">mass shift(s) in [Da] to search for </div><div class="ttdef"><b>Definition:</b> SILACFilter.h:68</div></div>
170
<div class="ttc" id="classOpenMS_1_1SILACFilter_html_ac6bad96f1ef902eafcbd7471bfced374"><div class="ttname"><a href="classOpenMS_1_1SILACFilter.html#ac6bad96f1ef902eafcbd7471bfced374">OpenMS::SILACFilter::elements_</a></div><div class="ttdeci">std::vector< SILACPattern > elements_</div><div class="ttdoc">holds the recognized features </div><div class="ttdef"><b>Definition:</b> SILACFilter.h:133</div></div>
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<div class="ttc" id="classOpenMS_1_1SILACFilter_html_a77a4124bcddddbacc0cb5a08a8204211"><div class="ttname"><a href="classOpenMS_1_1SILACFilter.html#a77a4124bcddddbacc0cb5a08a8204211">OpenMS::SILACFilter::number_of_peptides_</a></div><div class="ttdeci">Size number_of_peptides_</div><div class="ttdoc">number of peptides [i.e. number of labelled peptides +1, e.g. for SILAC triplet =3] ...</div><div class="ttdef"><b>Definition:</b> SILACFilter.h:108</div></div>
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<div class="ttc" id="classOpenMS_1_1SILACFilter_html_a8ab5115f2ddcdd7a96ca0186716af877"><div class="ttname"><a href="classOpenMS_1_1SILACFilter.html#a8ab5115f2ddcdd7a96ca0186716af877">OpenMS::SILACFilter::current_mz_</a></div><div class="ttdeci">DoubleReal current_mz_</div><div class="ttdoc">m/z at which the filter is currently applied to </div><div class="ttdef"><b>Definition:</b> SILACFilter.h:138</div></div>
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<div class="ttc" id="classOpenMS_1_1SILACFilter_html_af1b731c7f8e6095c30ed0b7148eaf16e"><div class="ttname"><a href="classOpenMS_1_1SILACFilter.html#af1b731c7f8e6095c30ed0b7148eaf16e">OpenMS::SILACFilter::peak_positions_</a></div><div class="ttdeci">std::vector< DoubleReal > peak_positions_</div><div class="ttdoc">peak positions of SILAC pattern </div><div class="ttdef"><b>Definition:</b> SILACFilter.h:113</div></div>
174
<div class="ttc" id="classOpenMS_1_1SILACFilter_html_af87dc576f79e04d5c793759410bb32f0"><div class="ttname"><a href="classOpenMS_1_1SILACFilter.html#af87dc576f79e04d5c793759410bb32f0">OpenMS::SILACFilter::exact_mz_positions_</a></div><div class="ttdeci">std::vector< std::vector< DoubleReal > > exact_mz_positions_</div><div class="ttdoc">m/z positions mz + exact_shifts in a SILAC pattern, where mz is the m/z of the mono-isotopic peak of ...</div><div class="ttdef"><b>Definition:</b> SILACFilter.h:148</div></div>
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<div class="ttc" id="classOpenMS_1_1SILACFiltering_1_1SpectrumInterpolation_html"><div class="ttname"><a href="classOpenMS_1_1SILACFiltering_1_1SpectrumInterpolation.html">OpenMS::SILACFiltering::SpectrumInterpolation</a></div><div class="ttdoc">Wrapper class for spectrum interpolation. </div><div class="ttdef"><b>Definition:</b> SILACFiltering.h:76</div></div>
176
<div class="ttc" id="classOpenMS_1_1SILACFilter_html_a2137970416910409891f9a50c918630d"><div class="ttname"><a href="classOpenMS_1_1SILACFilter.html#a2137970416910409891f9a50c918630d">OpenMS::SILACFilter::expected_mz_shifts_</a></div><div class="ttdeci">std::vector< DoubleReal > expected_mz_shifts_</div><div class="ttdoc">m/z shifts relative to mono-isotopic peak of unlabelled peptide </div><div class="ttdef"><b>Definition:</b> SILACFilter.h:123</div></div>
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<div class="ttc" id="classOpenMS_1_1SILACFilter_html_a15861ea59b6250c5078ff42021d25d5a"><div class="ttname"><a href="classOpenMS_1_1SILACFilter.html#a15861ea59b6250c5078ff42021d25d5a">OpenMS::SILACFilter::exact_intensities_</a></div><div class="ttdeci">std::vector< std::vector< DoubleReal > > exact_intensities_</div><div class="ttdoc">intensities at mz + exact_shifts in a SILAC pattern, where mz is the m/z of the mono-isotopic peak of...</div><div class="ttdef"><b>Definition:</b> SILACFilter.h:153</div></div>
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<div class="ttc" id="classOpenMS_1_1SILACFilter_html_ac82a29983c547ce48303395ccd6362d0"><div class="ttname"><a href="classOpenMS_1_1SILACFilter.html#ac82a29983c547ce48303395ccd6362d0">OpenMS::SILACFilter::intensity_correlation_</a></div><div class="ttdeci">DoubleReal intensity_correlation_</div><div class="ttdoc">minimal intensity correlation between regions of different peaks </div><div class="ttdef"><b>Definition:</b> SILACFilter.h:93</div></div>
179
<div class="ttc" id="classOpenMS_1_1SILACFilter_html_af71274961d8487036283991f2ba652a1"><div class="ttname"><a href="classOpenMS_1_1SILACFilter.html#af71274961d8487036283991f2ba652a1">OpenMS::SILACFilter::charge_</a></div><div class="ttdeci">Int charge_</div><div class="ttdoc">charge of the ions to search for </div><div class="ttdef"><b>Definition:</b> SILACFilter.h:73</div></div>
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<div class="ttc" id="group__Concept_html_gaf9ecec2d692138fab9167164a457cbd4"><div class="ttname"><a href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">OpenMS::Size</a></div><div class="ttdeci">size_t Size</div><div class="ttdoc">Size type e.g. used as variable which can hold result of size() </div><div class="ttdef"><b>Definition:</b> Types.h:144</div></div>
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<div class="ttc" id="classOpenMS_1_1SILACFilter_html_a13ba56ed55f3af6673f1f8799f2302bb"><div class="ttname"><a href="classOpenMS_1_1SILACFilter.html#a13ba56ed55f3af6673f1f8799f2302bb">OpenMS::SILACFilter::TheoreticalIsotopePattern</a></div><div class="ttdeci">IsotopeDistributionCache::TheoreticalIsotopePattern TheoreticalIsotopePattern</div><div class="ttdef"><b>Definition:</b> SILACFilter.h:63</div></div>
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<div class="ttc" id="classOpenMS_1_1SILACPattern_html"><div class="ttname"><a href="classOpenMS_1_1SILACPattern.html">OpenMS::SILACPattern</a></div><div class="ttdoc">A single SILAC pattern containing multiple found points. </div><div class="ttdef"><b>Definition:</b> SILACPattern.h:47</div></div>
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<div class="ttc" id="classOpenMS_1_1SILACFilter_html_af1be142aa6415d3b1a5cc6f961ceaa41"><div class="ttname"><a href="classOpenMS_1_1SILACFilter.html#af1be142aa6415d3b1a5cc6f961ceaa41">OpenMS::SILACFilter::mz_peptide_separations_</a></div><div class="ttdeci">std::vector< DoubleReal > mz_peptide_separations_</div><div class="ttdoc">m/z separtion between individual peptides [e.g. {0 Th, 4 Th, 5 Th}] </div><div class="ttdef"><b>Definition:</b> SILACFilter.h:118</div></div>
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<div class="ttc" id="classOpenMS_1_1IsotopeDistributionCache_html"><div class="ttname"><a href="classOpenMS_1_1IsotopeDistributionCache.html">OpenMS::IsotopeDistributionCache</a></div><div class="ttdoc">Prealculate isotope distributions for interesting mass ranges. </div><div class="ttdef"><b>Definition:</b> IsotopeDistributionCache.h:46</div></div>
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<div class="ttc" id="group__Concept_html_ga7cc214a236ad3bb6ad435bdcf5262a3f"><div class="ttname"><a href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">OpenMS::Int</a></div><div class="ttdeci">int Int</div><div class="ttdoc">Signed integer type. </div><div class="ttdef"><b>Definition:</b> Types.h:100</div></div>
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<div class="ttc" id="classOpenMS_1_1SILACFilter_html_ab3412d59616219275e3e08165981e169"><div class="ttname"><a href="classOpenMS_1_1SILACFilter.html#ab3412d59616219275e3e08165981e169">OpenMS::SILACFilter::expected_shifts_</a></div><div class="ttdeci">std::vector< std::vector< DoubleReal > > expected_shifts_</div><div class="ttdoc">expected m/z shift of isotopic peaks in a SILAC pattern relative to the mono-isotopic peak of the lig...</div><div class="ttdef"><b>Definition:</b> SILACFilter.h:158</div></div>
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<div class="ttc" id="classOpenMS_1_1SILACFiltering_html"><div class="ttname"><a href="classOpenMS_1_1SILACFiltering.html">OpenMS::SILACFiltering</a></div><div class="ttdoc">Filtering for SILAC data. </div><div class="ttdef"><b>Definition:</b> SILACFiltering.h:62</div></div>
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<div class="ttc" id="SILACPattern_8h_html"><div class="ttname"><a href="SILACPattern_8h.html">SILACPattern.h</a></div></div>
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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 11:19:20 using doxygen 1.8.5</font></TD>
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