File: ConfidenceScoring_8h_source.html

package info (click to toggle)
openms 1.11.1-5
  • links: PTS, VCS
  • area: main
  • in suites: jessie, jessie-kfreebsd
  • size: 436,688 kB
  • ctags: 150,907
  • sloc: cpp: 387,126; xml: 71,547; python: 7,764; ansic: 2,626; php: 2,499; sql: 737; ruby: 342; sh: 325; makefile: 128
file content (288 lines) | stat: -rw-r--r-- 52,112 bytes parent folder | download 
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
 
<HTML>
<HEAD>
<TITLE>ConfidenceScoring.h Source File</TITLE>
<LINK HREF="doxygen.css" REL="stylesheet" TYPE="text/css">
<LINK HREF="style_ini.css" REL="stylesheet" TYPE="text/css">
</HEAD>
<BODY BGCOLOR="#FFFFFF">
<A href="index.html">Home</A> &nbsp;&middot;
<A href="classes.html">Classes</A> &nbsp;&middot;
<A href="annotated.html">Annotated Classes</A> &nbsp;&middot;
<A href="modules.html">Modules</A> &nbsp;&middot;
<A href="functions_func.html">Members</A> &nbsp;&middot;
<A href="namespaces.html">Namespaces</A> &nbsp;&middot;
<A href="pages.html">Related Pages</A>
<HR style="height:1px; border:none; border-top:1px solid #c0c0c0;">
<!-- Generated by Doxygen 1.8.5 -->
<div id="nav-path" class="navpath">
  <ul>
<li class="navelem"><a class="el" href="dir_e770f0cf77e550adde3f44739ef529fe.html">include</a></li><li class="navelem"><a class="el" href="dir_6a63c4937d4da007e55fff5dcf71e0f8.html">OpenMS</a></li><li class="navelem"><a class="el" href="dir_330fe73d44ce641f33dd6036f80161a5.html">ANALYSIS</a></li><li class="navelem"><a class="el" href="dir_cebea83b16d377be32dcb02fb88342dd.html">OPENSWATH</a></li>  </ul>
</div>
</div><!-- top -->
<div class="header">
  <div class="headertitle">
<div class="title">ConfidenceScoring.h</div>  </div>
</div><!--header-->
<div class="contents">
<a href="ConfidenceScoring_8h.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno">    1</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00002"></a><span class="lineno">    2</span>&#160;<span class="comment">//                   OpenMS -- Open-Source Mass Spectrometry</span></div>
<div class="line"><a name="l00003"></a><span class="lineno">    3</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00004"></a><span class="lineno">    4</span>&#160;<span class="comment">// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,</span></div>
<div class="line"><a name="l00005"></a><span class="lineno">    5</span>&#160;<span class="comment">// ETH Zurich, and Freie Universitaet Berlin 2002-2013.</span></div>
<div class="line"><a name="l00006"></a><span class="lineno">    6</span>&#160;<span class="comment">//</span></div>
<div class="line"><a name="l00007"></a><span class="lineno">    7</span>&#160;<span class="comment">// This software is released under a three-clause BSD license:</span></div>
<div class="line"><a name="l00008"></a><span class="lineno">    8</span>&#160;<span class="comment">//  * Redistributions of source code must retain the above copyright</span></div>
<div class="line"><a name="l00009"></a><span class="lineno">    9</span>&#160;<span class="comment">//    notice, this list of conditions and the following disclaimer.</span></div>
<div class="line"><a name="l00010"></a><span class="lineno">   10</span>&#160;<span class="comment">//  * Redistributions in binary form must reproduce the above copyright</span></div>
<div class="line"><a name="l00011"></a><span class="lineno">   11</span>&#160;<span class="comment">//    notice, this list of conditions and the following disclaimer in the</span></div>
<div class="line"><a name="l00012"></a><span class="lineno">   12</span>&#160;<span class="comment">//    documentation and/or other materials provided with the distribution.</span></div>
<div class="line"><a name="l00013"></a><span class="lineno">   13</span>&#160;<span class="comment">//  * Neither the name of any author or any participating institution</span></div>
<div class="line"><a name="l00014"></a><span class="lineno">   14</span>&#160;<span class="comment">//    may be used to endorse or promote products derived from this software</span></div>
<div class="line"><a name="l00015"></a><span class="lineno">   15</span>&#160;<span class="comment">//    without specific prior written permission.</span></div>
<div class="line"><a name="l00016"></a><span class="lineno">   16</span>&#160;<span class="comment">// For a full list of authors, refer to the file AUTHORS.</span></div>
<div class="line"><a name="l00017"></a><span class="lineno">   17</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00018"></a><span class="lineno">   18</span>&#160;<span class="comment">// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS &quot;AS IS&quot;</span></div>
<div class="line"><a name="l00019"></a><span class="lineno">   19</span>&#160;<span class="comment">// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE</span></div>
<div class="line"><a name="l00020"></a><span class="lineno">   20</span>&#160;<span class="comment">// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE</span></div>
<div class="line"><a name="l00021"></a><span class="lineno">   21</span>&#160;<span class="comment">// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING</span></div>
<div class="line"><a name="l00022"></a><span class="lineno">   22</span>&#160;<span class="comment">// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,</span></div>
<div class="line"><a name="l00023"></a><span class="lineno">   23</span>&#160;<span class="comment">// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,</span></div>
<div class="line"><a name="l00024"></a><span class="lineno">   24</span>&#160;<span class="comment">// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;</span></div>
<div class="line"><a name="l00025"></a><span class="lineno">   25</span>&#160;<span class="comment">// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,</span></div>
<div class="line"><a name="l00026"></a><span class="lineno">   26</span>&#160;<span class="comment">// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR</span></div>
<div class="line"><a name="l00027"></a><span class="lineno">   27</span>&#160;<span class="comment">// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF</span></div>
<div class="line"><a name="l00028"></a><span class="lineno">   28</span>&#160;<span class="comment">// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</span></div>
<div class="line"><a name="l00029"></a><span class="lineno">   29</span>&#160;<span class="comment">//</span></div>
<div class="line"><a name="l00030"></a><span class="lineno">   30</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00031"></a><span class="lineno">   31</span>&#160;<span class="comment">// $Maintainer: Hendrik Weisser $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160;<span class="comment">// $Authors: Hannes Roest, Hendrik Weisser $</span></div>
<div class="line"><a name="l00033"></a><span class="lineno">   33</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00034"></a><span class="lineno">   34</span>&#160;</div>
<div class="line"><a name="l00035"></a><span class="lineno">   35</span>&#160;<span class="preprocessor">#ifndef OPENMS_ANALYSIS_OPENSWATH_CONFIDENCESCORING</span></div>
<div class="line"><a name="l00036"></a><span class="lineno">   36</span>&#160;<span class="preprocessor"></span><span class="preprocessor">#define OPENMS_ANALYSIS_OPENSWATH_CONFIDENCESCORING</span></div>
<div class="line"><a name="l00037"></a><span class="lineno">   37</span>&#160;<span class="preprocessor"></span></div>
<div class="line"><a name="l00038"></a><span class="lineno">   38</span>&#160;<span class="preprocessor">#include &lt;cmath&gt;</span> <span class="comment">// for &quot;exp&quot;</span></div>
<div class="line"><a name="l00039"></a><span class="lineno">   39</span>&#160;<span class="preprocessor">#include &lt;ctime&gt;</span> <span class="comment">// for &quot;time&quot; (random number seed)</span></div>
<div class="line"><a name="l00040"></a><span class="lineno">   40</span>&#160;<span class="preprocessor">#include &lt;limits&gt;</span> <span class="comment">// for &quot;infinity&quot;</span></div>
<div class="line"><a name="l00041"></a><span class="lineno">   41</span>&#160;<span class="preprocessor">#include &lt;boost/bimap.hpp&gt;</span></div>
<div class="line"><a name="l00042"></a><span class="lineno">   42</span>&#160;<span class="preprocessor">#include &lt;boost/bimap/multiset_of.hpp&gt;</span></div>
<div class="line"><a name="l00043"></a><span class="lineno">   43</span>&#160;<span class="preprocessor">#include &lt;boost/random/uniform_int.hpp&gt;</span></div>
<div class="line"><a name="l00044"></a><span class="lineno">   44</span>&#160;<span class="preprocessor">#include &lt;boost/random/mersenne_twister.hpp&gt;</span></div>
<div class="line"><a name="l00045"></a><span class="lineno">   45</span>&#160;<span class="preprocessor">#include &lt;boost/random/variate_generator.hpp&gt;</span></div>
<div class="line"><a name="l00046"></a><span class="lineno">   46</span>&#160;</div>
<div class="line"><a name="l00047"></a><span class="lineno">   47</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="FeatureXMLFile_8h.html">OpenMS/FORMAT/FeatureXMLFile.h</a>&gt;</span></div>
<div class="line"><a name="l00048"></a><span class="lineno">   48</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="TraMLFile_8h.html">OpenMS/FORMAT/TraMLFile.h</a>&gt;</span></div>
<div class="line"><a name="l00049"></a><span class="lineno">   49</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="TransformationXMLFile_8h.html">OpenMS/FORMAT/TransformationXMLFile.h</a>&gt;</span></div>
<div class="line"><a name="l00050"></a><span class="lineno">   50</span>&#160;</div>
<div class="line"><a name="l00051"></a><span class="lineno">   51</span>&#160;<span class="preprocessor">#include &quot;<a class="code" href="Scoring_8h.html">OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/ALGO/Scoring.h</a>&quot;</span></div>
<div class="line"><a name="l00052"></a><span class="lineno">   52</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="TransformationDescription_8h.html">OpenMS/ANALYSIS/MAPMATCHING/TransformationDescription.h</a>&gt;</span></div>
<div class="line"><a name="l00053"></a><span class="lineno">   53</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="TargetedExperiment_8h.html">OpenMS/ANALYSIS/TARGETED/TargetedExperiment.h</a>&gt;</span></div>
<div class="line"><a name="l00054"></a><span class="lineno">   54</span>&#160;</div>
<div class="line"><a name="l00055"></a><span class="lineno">   55</span>&#160;<span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00056"></a><span class="lineno">   56</span>&#160;{</div>
<div class="line"><a name="l00057"></a><span class="lineno">   57</span>&#160;</div>
<div class="line"><a name="l00058"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ConfidenceScoring.html">   58</a></span>&#160;<span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1ConfidenceScoring.html">ConfidenceScoring</a> :</div>
<div class="line"><a name="l00059"></a><span class="lineno">   59</span>&#160;    <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a></div>
<div class="line"><a name="l00060"></a><span class="lineno">   60</span>&#160;{</div>
<div class="line"><a name="l00061"></a><span class="lineno">   61</span>&#160;<span class="keyword">public</span>:</div>
<div class="line"><a name="l00062"></a><span class="lineno">   62</span>&#160;</div>
<div class="line"><a name="l00064"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ConfidenceScoring.html#ada171267bc93641a67a963525c7cb4fe">   64</a></span>&#160;    <a class="code" href="classOpenMS_1_1ConfidenceScoring.html#ada171267bc93641a67a963525c7cb4fe">ConfidenceScoring</a>(<span class="keywordtype">bool</span> test_mode_=<span class="keyword">false</span>) :</div>
<div class="line"><a name="l00065"></a><span class="lineno">   65</span>&#160;      generator_(), rand_gen_(generator_, boost::uniform_int&lt;&gt;())</div>
<div class="line"><a name="l00066"></a><span class="lineno">   66</span>&#160;    {</div>
<div class="line"><a name="l00067"></a><span class="lineno">   67</span>&#160;      <span class="keywordflow">if</span> (!test_mode_) rand_gen_.engine().seed(time(0)); <span class="comment">// seed with current time</span></div>
<div class="line"><a name="l00068"></a><span class="lineno">   68</span>&#160;    }</div>
<div class="line"><a name="l00069"></a><span class="lineno">   69</span>&#160;</div>
<div class="line"><a name="l00070"></a><span class="lineno">   70</span>&#160;<span class="keyword">protected</span>:</div>
<div class="line"><a name="l00071"></a><span class="lineno">   71</span>&#160;</div>
<div class="line"><a name="l00073"></a><span class="lineno">   73</span>&#160;    <span class="keyword">typedef</span> boost::bimap&lt;DoubleReal, boost::bimaps::multiset_of&lt;DoubleReal&gt; &gt; </div>
<div class="line"><a name="l00074"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ConfidenceScoring.html#a1da31f4d5736626ad34414fa29fea125">   74</a></span>&#160;    <a class="code" href="classOpenMS_1_1ConfidenceScoring.html#a1da31f4d5736626ad34414fa29fea125">BimapType</a>;</div>
<div class="line"><a name="l00075"></a><span class="lineno">   75</span>&#160;</div>
<div class="line"><a name="l00077"></a><span class="lineno">   77</span>&#160;    <span class="keyword">struct</span></div>
<div class="line"><a name="l00078"></a><span class="lineno">   78</span>&#160;    {</div>
<div class="line"><a name="l00079"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ConfidenceScoring.html#af265dcca032c8d6abc23a827c9a4f248">   79</a></span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1ConfidenceScoring.html#af265dcca032c8d6abc23a827c9a4f248">intercept</a>;</div>
<div class="line"><a name="l00080"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ConfidenceScoring.html#a888c258d17bb022450eb4fa36d51b680">   80</a></span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1ConfidenceScoring.html#a888c258d17bb022450eb4fa36d51b680">rt_coef</a>;</div>
<div class="line"><a name="l00081"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ConfidenceScoring.html#a8659dba580adb9d1bfd7e401f09b9c9e">   81</a></span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1ConfidenceScoring.html#a8659dba580adb9d1bfd7e401f09b9c9e">int_coef</a>;</div>
<div class="line"><a name="l00082"></a><span class="lineno">   82</span>&#160;</div>
<div class="line"><a name="l00083"></a><span class="lineno">   83</span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> operator()(<a class="code" href="classdouble.html">DoubleReal</a> diff_rt, <a class="code" href="classdouble.html">DoubleReal</a> dist_int)</div>
<div class="line"><a name="l00084"></a><span class="lineno">   84</span>&#160;      {</div>
<div class="line"><a name="l00085"></a><span class="lineno">   85</span>&#160;        <a class="code" href="classdouble.html">DoubleReal</a> lm = intercept + rt_coef * diff_rt * diff_rt + </div>
<div class="line"><a name="l00086"></a><span class="lineno">   86</span>&#160;          int_coef * dist_int;</div>
<div class="line"><a name="l00087"></a><span class="lineno">   87</span>&#160;        <span class="keywordflow">return</span> 1.0 / (1.0 + exp(-lm));</div>
<div class="line"><a name="l00088"></a><span class="lineno">   88</span>&#160;      }</div>
<div class="line"><a name="l00089"></a><span class="lineno">   89</span>&#160;    } glm_;</div>
<div class="line"><a name="l00090"></a><span class="lineno">   90</span>&#160;</div>
<div class="line"><a name="l00092"></a><span class="lineno">   92</span>&#160;    <span class="keyword">struct</span></div>
<div class="line"><a name="l00093"></a><span class="lineno">   93</span>&#160;    {</div>
<div class="line"><a name="l00094"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ConfidenceScoring.html#af2bcc8fd271954861c54e9948238b607">   94</a></span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1ConfidenceScoring.html#af2bcc8fd271954861c54e9948238b607">min_rt</a>;</div>
<div class="line"><a name="l00095"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ConfidenceScoring.html#a939a68c9800eb2c9017f45c93f913c89">   95</a></span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1ConfidenceScoring.html#a939a68c9800eb2c9017f45c93f913c89">max_rt</a>;</div>
<div class="line"><a name="l00096"></a><span class="lineno">   96</span>&#160;      </div>
<div class="line"><a name="l00097"></a><span class="lineno">   97</span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> operator()(<a class="code" href="classdouble.html">DoubleReal</a> rt)</div>
<div class="line"><a name="l00098"></a><span class="lineno">   98</span>&#160;      {</div>
<div class="line"><a name="l00099"></a><span class="lineno">   99</span>&#160;        <span class="keywordflow">return</span> (rt - min_rt) / (max_rt - min_rt) * 100;</div>
<div class="line"><a name="l00100"></a><span class="lineno">  100</span>&#160;      }</div>
<div class="line"><a name="l00101"></a><span class="lineno">  101</span>&#160;    } rt_norm_;</div>
<div class="line"><a name="l00102"></a><span class="lineno">  102</span>&#160;</div>
<div class="line"><a name="l00103"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ConfidenceScoring.html#a51890a436992cc17a97e6fcfc83a1479">  103</a></span>&#160;    <a class="code" href="classOpenMS_1_1TargetedExperiment.html">TargetedExperiment</a> <a class="code" href="classOpenMS_1_1ConfidenceScoring.html#a51890a436992cc17a97e6fcfc83a1479">library_</a>; <span class="comment">// assay library</span></div>
<div class="line"><a name="l00104"></a><span class="lineno">  104</span>&#160;</div>
<div class="line"><a name="l00105"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ConfidenceScoring.html#a55bfb4ab0325a76f4314692cfec6d0e2">  105</a></span>&#160;    <a class="code" href="classOpenMS_1_1IntList.html">IntList</a> <a class="code" href="classOpenMS_1_1ConfidenceScoring.html#a55bfb4ab0325a76f4314692cfec6d0e2">decoy_index_</a>; <span class="comment">// indexes of assays to use as decoys</span></div>
<div class="line"><a name="l00106"></a><span class="lineno">  106</span>&#160;</div>
<div class="line"><a name="l00107"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ConfidenceScoring.html#a5ed5e9c0515866ff61fe08664d36976f">  107</a></span>&#160;    <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="classOpenMS_1_1ConfidenceScoring.html#a5ed5e9c0515866ff61fe08664d36976f">n_decoys_</a>; <span class="comment">// number of decoys to use (per feature/true assay)</span></div>
<div class="line"><a name="l00108"></a><span class="lineno">  108</span>&#160;</div>
<div class="line"><a name="l00109"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ConfidenceScoring.html#ac39ec208bc01fe7c3c42ef7b01ed6cf9">  109</a></span>&#160;    <a class="code" href="classOpenMS_1_1Map.html">Map&lt;String, IntList&gt;</a> <a class="code" href="classOpenMS_1_1ConfidenceScoring.html#ac39ec208bc01fe7c3c42ef7b01ed6cf9">transition_map_</a>; <span class="comment">// assay (ID) -&gt; transitions (indexes)</span></div>
<div class="line"><a name="l00110"></a><span class="lineno">  110</span>&#160;</div>
<div class="line"><a name="l00111"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ConfidenceScoring.html#aec5b8fc65bc618a683989404f3db9fd2">  111</a></span>&#160;    <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="classOpenMS_1_1ConfidenceScoring.html#aec5b8fc65bc618a683989404f3db9fd2">n_transitions_</a>; <span class="comment">// number of transitions to consider</span></div>
<div class="line"><a name="l00112"></a><span class="lineno">  112</span>&#160;</div>
<div class="line"><a name="l00114"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ConfidenceScoring.html#a893246275c8a2c59ed7a23d062b70412">  114</a></span>&#160;    <a class="code" href="classOpenMS_1_1TransformationDescription.html">TransformationDescription</a> <a class="code" href="classOpenMS_1_1ConfidenceScoring.html#a893246275c8a2c59ed7a23d062b70412">rt_trafo_</a>;</div>
<div class="line"><a name="l00115"></a><span class="lineno">  115</span>&#160;</div>
<div class="line"><a name="l00116"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ConfidenceScoring.html#aaa12a78ed2e66fc3b1f20388d5f80145">  116</a></span>&#160;    boost::mt19937 <a class="code" href="classOpenMS_1_1ConfidenceScoring.html#aaa12a78ed2e66fc3b1f20388d5f80145">generator_</a>; <span class="comment">// random number generation engine</span></div>
<div class="line"><a name="l00117"></a><span class="lineno">  117</span>&#160;</div>
<div class="line"><a name="l00119"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ConfidenceScoring.html#a565f3f62b93681901b2582a5678cb3bf">  119</a></span>&#160;    boost::variate_generator&lt;boost::mt19937&amp;, boost::uniform_int&lt;&gt; &gt; <a class="code" href="classOpenMS_1_1ConfidenceScoring.html#a565f3f62b93681901b2582a5678cb3bf">rand_gen_</a>;</div>
<div class="line"><a name="l00120"></a><span class="lineno">  120</span>&#160;</div>
<div class="line"><a name="l00122"></a><span class="lineno">  122</span>&#160;    <span class="keywordtype">void</span> chooseDecoys_();</div>
<div class="line"><a name="l00123"></a><span class="lineno">  123</span>&#160;</div>
<div class="line"><a name="l00125"></a><span class="lineno">  125</span>&#160;    <a class="code" href="classdouble.html">DoubleReal</a> manhattanDist_(<a class="code" href="classOpenMS_1_1DoubleList.html">DoubleList</a> x, <a class="code" href="classOpenMS_1_1DoubleList.html">DoubleList</a> y);</div>
<div class="line"><a name="l00126"></a><span class="lineno">  126</span>&#160;</div>
<div class="line"><a name="l00128"></a><span class="lineno">  128</span>&#160;    <a class="code" href="classdouble.html">DoubleReal</a> getAssayRT_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1TargetedExperimentHelper_1_1Peptide.html">TargetedExperiment::Peptide</a>&amp; assay,</div>
<div class="line"><a name="l00129"></a><span class="lineno">  129</span>&#160;                           <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>&amp; cv_accession = <span class="stringliteral">&quot;MS:1000896&quot;</span>);</div>
<div class="line"><a name="l00130"></a><span class="lineno">  130</span>&#160;</div>
<div class="line"><a name="l00133"></a><span class="lineno">  133</span>&#160;    <span class="keywordtype">void</span> extractIntensities_(<a class="code" href="classOpenMS_1_1ConfidenceScoring.html#a1da31f4d5736626ad34414fa29fea125">BimapType</a>&amp; intensity_map, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> n_transitions,</div>
<div class="line"><a name="l00134"></a><span class="lineno">  134</span>&#160;                             <a class="code" href="classOpenMS_1_1DoubleList.html">DoubleList</a>&amp; intensities);</div>
<div class="line"><a name="l00135"></a><span class="lineno">  135</span>&#160;</div>
<div class="line"><a name="l00139"></a><span class="lineno">  139</span>&#160;    <a class="code" href="classdouble.html">DoubleReal</a> scoreAssay_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1TargetedExperimentHelper_1_1Peptide.html">TargetedExperiment::Peptide</a>&amp; assay, </div>
<div class="line"><a name="l00140"></a><span class="lineno">  140</span>&#160;                           <a class="code" href="classdouble.html">DoubleReal</a> feature_rt, <a class="code" href="classOpenMS_1_1DoubleList.html">DoubleList</a>&amp; feature_intensities,</div>
<div class="line"><a name="l00141"></a><span class="lineno">  141</span>&#160;                           <span class="keyword">const</span> std::set&lt;String&gt;&amp; transition_ids = std::set&lt;String&gt;());</div>
<div class="line"><a name="l00142"></a><span class="lineno">  142</span>&#160;</div>
<div class="line"><a name="l00144"></a><span class="lineno">  144</span>&#160;    <span class="keywordtype">void</span> scoreFeature_(<a class="code" href="classOpenMS_1_1Feature.html">Feature</a>&amp; feature);</div>
<div class="line"><a name="l00145"></a><span class="lineno">  145</span>&#160;</div>
<div class="line"><a name="l00146"></a><span class="lineno">  146</span>&#160;<span class="keyword">public</span>:</div>
<div class="line"><a name="l00147"></a><span class="lineno">  147</span>&#160;</div>
<div class="line"><a name="l00148"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ConfidenceScoring.html#ae5c59a6fcececb0ea4c238c6d303262f">  148</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1ConfidenceScoring.html#ae5c59a6fcececb0ea4c238c6d303262f">initialize</a>(<a class="code" href="classOpenMS_1_1TargetedExperiment.html">TargetedExperiment</a> library, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> n_decoys, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> n_transitions, <a class="code" href="classOpenMS_1_1TransformationDescription.html">TransformationDescription</a> rt_trafo)</div>
<div class="line"><a name="l00149"></a><span class="lineno">  149</span>&#160;    {</div>
<div class="line"><a name="l00150"></a><span class="lineno">  150</span>&#160;      library_ = <a class="code" href="classOpenMS_1_1TargetedExperiment.html">TargetedExperiment</a>(library); </div>
<div class="line"><a name="l00151"></a><span class="lineno">  151</span>&#160;      n_decoys_ = n_decoys;</div>
<div class="line"><a name="l00152"></a><span class="lineno">  152</span>&#160;      n_transitions_ = n_transitions;</div>
<div class="line"><a name="l00153"></a><span class="lineno">  153</span>&#160;      rt_trafo_ = rt_trafo;</div>
<div class="line"><a name="l00154"></a><span class="lineno">  154</span>&#160;    }</div>
<div class="line"><a name="l00155"></a><span class="lineno">  155</span>&#160;</div>
<div class="line"><a name="l00156"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ConfidenceScoring.html#ae1da64a2f1d78a414f0bdc70ca4bc883">  156</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1ConfidenceScoring.html#ae1da64a2f1d78a414f0bdc70ca4bc883">initializeGlm</a>(<span class="keywordtype">double</span> intercept, <span class="keywordtype">double</span> rt_coef, <span class="keywordtype">double</span> int_coef)</div>
<div class="line"><a name="l00157"></a><span class="lineno">  157</span>&#160;    {</div>
<div class="line"><a name="l00158"></a><span class="lineno">  158</span>&#160;      glm_.intercept = intercept;</div>
<div class="line"><a name="l00159"></a><span class="lineno">  159</span>&#160;      glm_.rt_coef = rt_coef;</div>
<div class="line"><a name="l00160"></a><span class="lineno">  160</span>&#160;      glm_.int_coef = int_coef;</div>
<div class="line"><a name="l00161"></a><span class="lineno">  161</span>&#160;    }</div>
<div class="line"><a name="l00162"></a><span class="lineno">  162</span>&#160;</div>
<div class="line"><a name="l00175"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ConfidenceScoring.html#ae432ca06f1c61329d4dff693498b6996">  175</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1ConfidenceScoring.html#ae432ca06f1c61329d4dff693498b6996">scoreMap</a>(<a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap&lt;&gt;</a> &amp; features)</div>
<div class="line"><a name="l00176"></a><span class="lineno">  176</span>&#160;    {</div>
<div class="line"><a name="l00177"></a><span class="lineno">  177</span>&#160;      <span class="comment">// are there enough assays in the library?</span></div>
<div class="line"><a name="l00178"></a><span class="lineno">  178</span>&#160;      <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> n_assays = library_.getPeptides().size();</div>
<div class="line"><a name="l00179"></a><span class="lineno">  179</span>&#160;      <span class="keywordflow">if</span> (n_assays &lt; 2)</div>
<div class="line"><a name="l00180"></a><span class="lineno">  180</span>&#160;      {</div>
<div class="line"><a name="l00181"></a><span class="lineno">  181</span>&#160;        <span class="keywordflow">throw</span> <a class="code" href="classOpenMS_1_1Exception_1_1IllegalArgument.html">Exception::IllegalArgument</a>(__FILE__, __LINE__, __PRETTY_FUNCTION__,</div>
<div class="line"><a name="l00182"></a><span class="lineno">  182</span>&#160;                                         <span class="stringliteral">&quot;There need to be at least 2 assays in the library for ConfidenceScoring.&quot;</span>);</div>
<div class="line"><a name="l00183"></a><span class="lineno">  183</span>&#160;</div>
<div class="line"><a name="l00184"></a><span class="lineno">  184</span>&#160;      }</div>
<div class="line"><a name="l00185"></a><span class="lineno">  185</span>&#160;      <span class="keywordflow">if</span> (n_assays - 1 &lt; n_decoys_)</div>
<div class="line"><a name="l00186"></a><span class="lineno">  186</span>&#160;      {</div>
<div class="line"><a name="l00187"></a><span class="lineno">  187</span>&#160;        <a class="code" href="LogStream_8h.html#aea3f57d6dcc5b4ac957e2679e87dde27">LOG_WARN</a> &lt;&lt; <span class="stringliteral">&quot;Warning: Parameter &#39;decoys&#39; (&quot;</span> &lt;&lt; n_decoys_ </div>
<div class="line"><a name="l00188"></a><span class="lineno">  188</span>&#160;                 &lt;&lt; <span class="stringliteral">&quot;) is higher than the number of unrelated assays in the &quot;</span></div>
<div class="line"><a name="l00189"></a><span class="lineno">  189</span>&#160;                 &lt;&lt; <span class="stringliteral">&quot;library (&quot;</span> &lt;&lt; n_assays - 1 &lt;&lt; <span class="stringliteral">&quot;). &quot;</span></div>
<div class="line"><a name="l00190"></a><span class="lineno">  190</span>&#160;                 &lt;&lt; <span class="stringliteral">&quot;Using all unrelated assays as decoys.&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a name="l00191"></a><span class="lineno">  191</span>&#160;      }</div>
<div class="line"><a name="l00192"></a><span class="lineno">  192</span>&#160;      <span class="keywordflow">if</span> (n_assays - 1 &lt;= n_decoys_) n_decoys_ = 0; <span class="comment">// use all available assays</span></div>
<div class="line"><a name="l00193"></a><span class="lineno">  193</span>&#160;</div>
<div class="line"><a name="l00194"></a><span class="lineno">  194</span>&#160;      decoy_index_.resize(n_assays);</div>
<div class="line"><a name="l00195"></a><span class="lineno">  195</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i &lt; n_assays; ++i) decoy_index_[i] = boost::numeric_cast&lt;Int&gt;(i);</div>
<div class="line"><a name="l00196"></a><span class="lineno">  196</span>&#160;</div>
<div class="line"><a name="l00197"></a><span class="lineno">  197</span>&#160;      <span class="comment">// build mapping between assays and transitions:</span></div>
<div class="line"><a name="l00198"></a><span class="lineno">  198</span>&#160;      <a class="code" href="LogStream_8h.html#a6ff63e8955665c4a58b1598f2b07c51a">LOG_DEBUG</a> &lt;&lt; <span class="stringliteral">&quot;Building transition map...&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a name="l00199"></a><span class="lineno">  199</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i &lt; library_.getTransitions().size(); ++i)</div>
<div class="line"><a name="l00200"></a><span class="lineno">  200</span>&#160;      {</div>
<div class="line"><a name="l00201"></a><span class="lineno">  201</span>&#160;        <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>&amp; ref = library_.getTransitions()[i].getPeptideRef();</div>
<div class="line"><a name="l00202"></a><span class="lineno">  202</span>&#160;        transition_map_[ref].push_back(boost::numeric_cast&lt;Int&gt;(i));</div>
<div class="line"><a name="l00203"></a><span class="lineno">  203</span>&#160;      }</div>
<div class="line"><a name="l00204"></a><span class="lineno">  204</span>&#160;      <span class="comment">// find min./max. RT in the library:</span></div>
<div class="line"><a name="l00205"></a><span class="lineno">  205</span>&#160;      <a class="code" href="LogStream_8h.html#a6ff63e8955665c4a58b1598f2b07c51a">LOG_DEBUG</a> &lt;&lt; <span class="stringliteral">&quot;Determining retention time range...&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a name="l00206"></a><span class="lineno">  206</span>&#160;      rt_norm_.min_rt = std::numeric_limits&lt;double&gt;::infinity();</div>
<div class="line"><a name="l00207"></a><span class="lineno">  207</span>&#160;      rt_norm_.max_rt = -std::numeric_limits&lt;double&gt;::infinity();</div>
<div class="line"><a name="l00208"></a><span class="lineno">  208</span>&#160;      <span class="keywordflow">for</span> (std::vector&lt;TargetedExperiment::Peptide&gt;::const_iterator it = </div>
<div class="line"><a name="l00209"></a><span class="lineno">  209</span>&#160;             library_.getPeptides().begin(); it != library_.getPeptides().end();</div>
<div class="line"><a name="l00210"></a><span class="lineno">  210</span>&#160;           ++it)</div>
<div class="line"><a name="l00211"></a><span class="lineno">  211</span>&#160;      {</div>
<div class="line"><a name="l00212"></a><span class="lineno">  212</span>&#160;        <a class="code" href="classdouble.html">DoubleReal</a> current_rt = getAssayRT_(*it);</div>
<div class="line"><a name="l00213"></a><span class="lineno">  213</span>&#160;        <span class="keywordflow">if</span> (current_rt == -1.0) <span class="keywordflow">continue</span>; <span class="comment">// indicates a missing value</span></div>
<div class="line"><a name="l00214"></a><span class="lineno">  214</span>&#160;        rt_norm_.min_rt = std::min(rt_norm_.min_rt, current_rt);</div>
<div class="line"><a name="l00215"></a><span class="lineno">  215</span>&#160;        rt_norm_.max_rt = std::max(rt_norm_.max_rt, current_rt);</div>
<div class="line"><a name="l00216"></a><span class="lineno">  216</span>&#160;      }</div>
<div class="line"><a name="l00217"></a><span class="lineno">  217</span>&#160;</div>
<div class="line"><a name="l00218"></a><span class="lineno">  218</span>&#160;      <span class="comment">// log scoring progress:</span></div>
<div class="line"><a name="l00219"></a><span class="lineno">  219</span>&#160;      <a class="code" href="LogStream_8h.html#a6ff63e8955665c4a58b1598f2b07c51a">LOG_DEBUG</a> &lt;&lt; <span class="stringliteral">&quot;Scoring features...&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a name="l00220"></a><span class="lineno">  220</span>&#160;      startProgress(0, features.size(), <span class="stringliteral">&quot;scoring features&quot;</span>);</div>
<div class="line"><a name="l00221"></a><span class="lineno">  221</span>&#160;</div>
<div class="line"><a name="l00222"></a><span class="lineno">  222</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap&lt;&gt;::Iterator</a> feat_it = features.begin(); </div>
<div class="line"><a name="l00223"></a><span class="lineno">  223</span>&#160;           feat_it != features.end(); ++feat_it)</div>
<div class="line"><a name="l00224"></a><span class="lineno">  224</span>&#160;      {</div>
<div class="line"><a name="l00225"></a><span class="lineno">  225</span>&#160;        <a class="code" href="LogStream_8h.html#a6ff63e8955665c4a58b1598f2b07c51a">LOG_DEBUG</a> &lt;&lt; <span class="stringliteral">&quot;Feature &quot;</span> &lt;&lt; feat_it - features.begin() + 1 </div>
<div class="line"><a name="l00226"></a><span class="lineno">  226</span>&#160;                  &lt;&lt; <span class="stringliteral">&quot; (ID &#39;&quot;</span> &lt;&lt; feat_it-&gt;<a class="code" href="classOpenMS_1_1UniqueIdInterface.html#a0a9d0893724cca92411b6051f4ce3e16">getUniqueId</a>() &lt;&lt; <span class="stringliteral">&quot;&#39;)&quot;</span>&lt;&lt; std::endl;</div>
<div class="line"><a name="l00227"></a><span class="lineno">  227</span>&#160;        scoreFeature_(*feat_it);</div>
<div class="line"><a name="l00228"></a><span class="lineno">  228</span>&#160;        setProgress(feat_it - features.begin());</div>
<div class="line"><a name="l00229"></a><span class="lineno">  229</span>&#160;      }</div>
<div class="line"><a name="l00230"></a><span class="lineno">  230</span>&#160;      endProgress();</div>
<div class="line"><a name="l00231"></a><span class="lineno">  231</span>&#160;</div>
<div class="line"><a name="l00232"></a><span class="lineno">  232</span>&#160;    }</div>
<div class="line"><a name="l00233"></a><span class="lineno">  233</span>&#160;</div>
<div class="line"><a name="l00234"></a><span class="lineno">  234</span>&#160;};</div>
<div class="line"><a name="l00235"></a><span class="lineno">  235</span>&#160;</div>
<div class="line"><a name="l00236"></a><span class="lineno">  236</span>&#160;}</div>
<div class="line"><a name="l00237"></a><span class="lineno">  237</span>&#160;</div>
<div class="line"><a name="l00238"></a><span class="lineno">  238</span>&#160;<span class="preprocessor">#endif // OPENMS_ANALYSIS_OPENSWATH_CONFIDENCESCORING</span></div>
<div class="ttc" id="classOpenMS_1_1ConfidenceScoring_html_a888c258d17bb022450eb4fa36d51b680"><div class="ttname"><a href="classOpenMS_1_1ConfidenceScoring.html#a888c258d17bb022450eb4fa36d51b680">OpenMS::ConfidenceScoring::rt_coef</a></div><div class="ttdeci">DoubleReal rt_coef</div><div class="ttdef"><b>Definition:</b> ConfidenceScoring.h:80</div></div>
<div class="ttc" id="FeatureXMLFile_8h_html"><div class="ttname"><a href="FeatureXMLFile_8h.html">FeatureXMLFile.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1String_html"><div class="ttname"><a href="classOpenMS_1_1String.html">OpenMS::String</a></div><div class="ttdoc">A more convenient string class. </div><div class="ttdef"><b>Definition:</b> String.h:56</div></div>
<div class="ttc" id="classOpenMS_1_1ConfidenceScoring_html_ae1da64a2f1d78a414f0bdc70ca4bc883"><div class="ttname"><a href="classOpenMS_1_1ConfidenceScoring.html#ae1da64a2f1d78a414f0bdc70ca4bc883">OpenMS::ConfidenceScoring::initializeGlm</a></div><div class="ttdeci">void initializeGlm(double intercept, double rt_coef, double int_coef)</div><div class="ttdef"><b>Definition:</b> ConfidenceScoring.h:156</div></div>
<div class="ttc" id="classOpenMS_1_1ConfidenceScoring_html_af2bcc8fd271954861c54e9948238b607"><div class="ttname"><a href="classOpenMS_1_1ConfidenceScoring.html#af2bcc8fd271954861c54e9948238b607">OpenMS::ConfidenceScoring::min_rt</a></div><div class="ttdeci">DoubleReal min_rt</div><div class="ttdef"><b>Definition:</b> ConfidenceScoring.h:94</div></div>
<div class="ttc" id="classOpenMS_1_1ConfidenceScoring_html_a8659dba580adb9d1bfd7e401f09b9c9e"><div class="ttname"><a href="classOpenMS_1_1ConfidenceScoring.html#a8659dba580adb9d1bfd7e401f09b9c9e">OpenMS::ConfidenceScoring::int_coef</a></div><div class="ttdeci">DoubleReal int_coef</div><div class="ttdef"><b>Definition:</b> ConfidenceScoring.h:81</div></div>
<div class="ttc" id="Scoring_8h_html"><div class="ttname"><a href="Scoring_8h.html">Scoring.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1FeatureMap_html"><div class="ttname"><a href="classOpenMS_1_1FeatureMap.html">OpenMS::FeatureMap&lt;&gt;</a></div></div>
<div class="ttc" id="classOpenMS_1_1ConfidenceScoring_html_ae432ca06f1c61329d4dff693498b6996"><div class="ttname"><a href="classOpenMS_1_1ConfidenceScoring.html#ae432ca06f1c61329d4dff693498b6996">OpenMS::ConfidenceScoring::scoreMap</a></div><div class="ttdeci">void scoreMap(FeatureMap&lt;&gt; &amp;features)</div><div class="ttdoc">Score a feature map -&amp;gt; make sure the class is properly initialized. </div><div class="ttdef"><b>Definition:</b> ConfidenceScoring.h:175</div></div>
<div class="ttc" id="classdouble_html"><div class="ttname"><a href="classdouble.html">double</a></div></div>
<div class="ttc" id="classOpenMS_1_1ConfidenceScoring_html_ac39ec208bc01fe7c3c42ef7b01ed6cf9"><div class="ttname"><a href="classOpenMS_1_1ConfidenceScoring.html#ac39ec208bc01fe7c3c42ef7b01ed6cf9">OpenMS::ConfidenceScoring::transition_map_</a></div><div class="ttdeci">Map&lt; String, IntList &gt; transition_map_</div><div class="ttdef"><b>Definition:</b> ConfidenceScoring.h:109</div></div>
<div class="ttc" id="LogStream_8h_html_a6ff63e8955665c4a58b1598f2b07c51a"><div class="ttname"><a href="LogStream_8h.html#a6ff63e8955665c4a58b1598f2b07c51a">LOG_DEBUG</a></div><div class="ttdeci">#define LOG_DEBUG</div><div class="ttdoc">Macro for general debugging information. </div><div class="ttdef"><b>Definition:</b> LogStream.h:459</div></div>
<div class="ttc" id="LogStream_8h_html_aea3f57d6dcc5b4ac957e2679e87dde27"><div class="ttname"><a href="LogStream_8h.html#aea3f57d6dcc5b4ac957e2679e87dde27">LOG_WARN</a></div><div class="ttdeci">#define LOG_WARN</div><div class="ttdoc">Macro if a warning, a piece of information which should be read by the user, should be logged...</div><div class="ttdef"><b>Definition:</b> LogStream.h:451</div></div>
<div class="ttc" id="classOpenMS_1_1ConfidenceScoring_html_a51890a436992cc17a97e6fcfc83a1479"><div class="ttname"><a href="classOpenMS_1_1ConfidenceScoring.html#a51890a436992cc17a97e6fcfc83a1479">OpenMS::ConfidenceScoring::library_</a></div><div class="ttdeci">TargetedExperiment library_</div><div class="ttdef"><b>Definition:</b> ConfidenceScoring.h:103</div></div>
<div class="ttc" id="classOpenMS_1_1ConfidenceScoring_html_a893246275c8a2c59ed7a23d062b70412"><div class="ttname"><a href="classOpenMS_1_1ConfidenceScoring.html#a893246275c8a2c59ed7a23d062b70412">OpenMS::ConfidenceScoring::rt_trafo_</a></div><div class="ttdeci">TransformationDescription rt_trafo_</div><div class="ttdoc">RT transformation to map measured RTs to assay RTs. </div><div class="ttdef"><b>Definition:</b> ConfidenceScoring.h:114</div></div>
<div class="ttc" id="classOpenMS_1_1ConfidenceScoring_html_aaa12a78ed2e66fc3b1f20388d5f80145"><div class="ttname"><a href="classOpenMS_1_1ConfidenceScoring.html#aaa12a78ed2e66fc3b1f20388d5f80145">OpenMS::ConfidenceScoring::generator_</a></div><div class="ttdeci">boost::mt19937 generator_</div><div class="ttdef"><b>Definition:</b> ConfidenceScoring.h:116</div></div>
<div class="ttc" id="classOpenMS_1_1ConfidenceScoring_html_a939a68c9800eb2c9017f45c93f913c89"><div class="ttname"><a href="classOpenMS_1_1ConfidenceScoring.html#a939a68c9800eb2c9017f45c93f913c89">OpenMS::ConfidenceScoring::max_rt</a></div><div class="ttdeci">DoubleReal max_rt</div><div class="ttdef"><b>Definition:</b> ConfidenceScoring.h:95</div></div>
<div class="ttc" id="classOpenMS_1_1Exception_1_1IllegalArgument_html"><div class="ttname"><a href="classOpenMS_1_1Exception_1_1IllegalArgument.html">OpenMS::Exception::IllegalArgument</a></div><div class="ttdoc">A method or algorithm argument contains illegal values. </div><div class="ttdef"><b>Definition:</b> Exception.h:634</div></div>
<div class="ttc" id="classOpenMS_1_1ConfidenceScoring_html_ada171267bc93641a67a963525c7cb4fe"><div class="ttname"><a href="classOpenMS_1_1ConfidenceScoring.html#ada171267bc93641a67a963525c7cb4fe">OpenMS::ConfidenceScoring::ConfidenceScoring</a></div><div class="ttdeci">ConfidenceScoring(bool test_mode_=false)</div><div class="ttdoc">Constructor. </div><div class="ttdef"><b>Definition:</b> ConfidenceScoring.h:64</div></div>
<div class="ttc" id="classOpenMS_1_1ConfidenceScoring_html_af265dcca032c8d6abc23a827c9a4f248"><div class="ttname"><a href="classOpenMS_1_1ConfidenceScoring.html#af265dcca032c8d6abc23a827c9a4f248">OpenMS::ConfidenceScoring::intercept</a></div><div class="ttdeci">DoubleReal intercept</div><div class="ttdef"><b>Definition:</b> ConfidenceScoring.h:79</div></div>
<div class="ttc" id="TargetedExperiment_8h_html"><div class="ttname"><a href="TargetedExperiment_8h.html">TargetedExperiment.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1ConfidenceScoring_html_a55bfb4ab0325a76f4314692cfec6d0e2"><div class="ttname"><a href="classOpenMS_1_1ConfidenceScoring.html#a55bfb4ab0325a76f4314692cfec6d0e2">OpenMS::ConfidenceScoring::decoy_index_</a></div><div class="ttdeci">IntList decoy_index_</div><div class="ttdef"><b>Definition:</b> ConfidenceScoring.h:105</div></div>
<div class="ttc" id="classOpenMS_1_1Feature_html"><div class="ttname"><a href="classOpenMS_1_1Feature.html">OpenMS::Feature</a></div><div class="ttdoc">An LC-MS feature. </div><div class="ttdef"><b>Definition:</b> Feature.h:66</div></div>
<div class="ttc" id="classOpenMS_1_1ConfidenceScoring_html_ae5c59a6fcececb0ea4c238c6d303262f"><div class="ttname"><a href="classOpenMS_1_1ConfidenceScoring.html#ae5c59a6fcececb0ea4c238c6d303262f">OpenMS::ConfidenceScoring::initialize</a></div><div class="ttdeci">void initialize(TargetedExperiment library, Size n_decoys, Size n_transitions, TransformationDescription rt_trafo)</div><div class="ttdef"><b>Definition:</b> ConfidenceScoring.h:148</div></div>
<div class="ttc" id="classOpenMS_1_1ConfidenceScoring_html"><div class="ttname"><a href="classOpenMS_1_1ConfidenceScoring.html">OpenMS::ConfidenceScoring</a></div><div class="ttdef"><b>Definition:</b> ConfidenceScoring.h:58</div></div>
<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>
<div class="ttc" id="classOpenMS_1_1ConfidenceScoring_html_a5ed5e9c0515866ff61fe08664d36976f"><div class="ttname"><a href="classOpenMS_1_1ConfidenceScoring.html#a5ed5e9c0515866ff61fe08664d36976f">OpenMS::ConfidenceScoring::n_decoys_</a></div><div class="ttdeci">Size n_decoys_</div><div class="ttdef"><b>Definition:</b> ConfidenceScoring.h:107</div></div>
<div class="ttc" id="classOpenMS_1_1ConfidenceScoring_html_aec5b8fc65bc618a683989404f3db9fd2"><div class="ttname"><a href="classOpenMS_1_1ConfidenceScoring.html#aec5b8fc65bc618a683989404f3db9fd2">OpenMS::ConfidenceScoring::n_transitions_</a></div><div class="ttdeci">Size n_transitions_</div><div class="ttdef"><b>Definition:</b> ConfidenceScoring.h:111</div></div>
<div class="ttc" id="classOpenMS_1_1ProgressLogger_html"><div class="ttname"><a href="classOpenMS_1_1ProgressLogger.html">OpenMS::ProgressLogger</a></div><div class="ttdoc">Base class for all classes that want to report their progess. </div><div class="ttdef"><b>Definition:</b> ProgressLogger.h:56</div></div>
<div class="ttc" id="classOpenMS_1_1TargetedExperiment_html"><div class="ttname"><a href="classOpenMS_1_1TargetedExperiment.html">OpenMS::TargetedExperiment</a></div><div class="ttdoc">This class stores an prediction of an SRM/MRM transition. </div><div class="ttdef"><b>Definition:</b> TargetedExperiment.h:53</div></div>
<div class="ttc" id="TransformationDescription_8h_html"><div class="ttname"><a href="TransformationDescription_8h.html">TransformationDescription.h</a></div></div>
<div class="ttc" id="TraMLFile_8h_html"><div class="ttname"><a href="TraMLFile_8h.html">TraMLFile.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1TransformationDescription_html"><div class="ttname"><a href="classOpenMS_1_1TransformationDescription.html">OpenMS::TransformationDescription</a></div><div class="ttdoc">Generic description of a coordinate transformation. </div><div class="ttdef"><b>Definition:</b> TransformationDescription.h:59</div></div>
<div class="ttc" id="classOpenMS_1_1ConfidenceScoring_html_a565f3f62b93681901b2582a5678cb3bf"><div class="ttname"><a href="classOpenMS_1_1ConfidenceScoring.html#a565f3f62b93681901b2582a5678cb3bf">OpenMS::ConfidenceScoring::rand_gen_</a></div><div class="ttdeci">boost::variate_generator&lt; boost::mt19937 &amp;, boost::uniform_int&lt;&gt; &gt; rand_gen_</div><div class="ttdoc">Random number generator (must be initialized in init. list of c&amp;#39;tor!) </div><div class="ttdef"><b>Definition:</b> ConfidenceScoring.h:119</div></div>
<div class="ttc" id="TransformationXMLFile_8h_html"><div class="ttname"><a href="TransformationXMLFile_8h.html">TransformationXMLFile.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1Map_html"><div class="ttname"><a href="classOpenMS_1_1Map.html">OpenMS::Map</a></div><div class="ttdoc">Map class based on the STL map (containing serveral convenience functions) </div><div class="ttdef"><b>Definition:</b> Map.h:50</div></div>
<div class="ttc" id="classOpenMS_1_1UniqueIdInterface_html_a0a9d0893724cca92411b6051f4ce3e16"><div class="ttname"><a href="classOpenMS_1_1UniqueIdInterface.html#a0a9d0893724cca92411b6051f4ce3e16">OpenMS::UniqueIdInterface::getUniqueId</a></div><div class="ttdeci">UInt64 getUniqueId() const </div><div class="ttdoc">Non-mutable access to unique id - returns the unique id. </div><div class="ttdef"><b>Definition:</b> UniqueIdInterface.h:109</div></div>
<div class="ttc" id="classOpenMS_1_1DoubleList_html"><div class="ttname"><a href="classOpenMS_1_1DoubleList.html">OpenMS::DoubleList</a></div><div class="ttdoc">DoubleReal list. </div><div class="ttdef"><b>Definition:</b> DoubleList.h:56</div></div>
<div class="ttc" id="classOpenMS_1_1ConfidenceScoring_html_a1da31f4d5736626ad34414fa29fea125"><div class="ttname"><a href="classOpenMS_1_1ConfidenceScoring.html#a1da31f4d5736626ad34414fa29fea125">OpenMS::ConfidenceScoring::BimapType</a></div><div class="ttdeci">boost::bimap&lt; DoubleReal, boost::bimaps::multiset_of&lt; DoubleReal &gt; &gt; BimapType</div><div class="ttdoc">Mapping: Q3 m/z &amp;lt;-&amp;gt; transition intensity (maybe not unique!) </div><div class="ttdef"><b>Definition:</b> ConfidenceScoring.h:74</div></div>
<div class="ttc" id="classOpenMS_1_1TargetedExperimentHelper_1_1Peptide_html"><div class="ttname"><a href="classOpenMS_1_1TargetedExperimentHelper_1_1Peptide.html">OpenMS::TargetedExperimentHelper::Peptide</a></div><div class="ttdef"><b>Definition:</b> TargetedExperimentHelper.h:211</div></div>
<div class="ttc" id="classOpenMS_1_1IntList_html"><div class="ttname"><a href="classOpenMS_1_1IntList.html">OpenMS::IntList</a></div><div class="ttdoc">Int list. </div><div class="ttdef"><b>Definition:</b> IntList.h:56</div></div>
</div><!-- fragment --></div><!-- contents -->
<HR style="height:1px; border:none; border-top:1px solid #c0c0c0;">
<TABLE width="100%" border="0">
<TR>
<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:12 using doxygen 1.8.5</font></TD>
</TR>
</TABLE>
</BODY>
</HTML>