File: FeatureFinderAlgorithmSimple_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 (333 lines) | stat: -rw-r--r-- 71,363 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
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
 
<HTML>
<HEAD>
<TITLE>FeatureFinderAlgorithmSimple.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_9f700962877a340cb515a8f4e78fa50c.html">TRANSFORMATIONS</a></li><li class="navelem"><a class="el" href="dir_37e9c1b52d0b253b62f883ccdf65930c.html">FEATUREFINDER</a></li>  </ul>
</div>
</div><!-- top -->
<div class="header">
  <div class="headertitle">
<div class="title">FeatureFinderAlgorithmSimple.h</div>  </div>
</div><!--header-->
<div class="contents">
<a href="FeatureFinderAlgorithmSimple_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: Clemens Groepl $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160;<span class="comment">// $Authors: $</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_TRANSFORMATIONS_FEATUREFINDER_FEATUREFINDERALGORITHMSIMPLE_H</span></div>
<div class="line"><a name="l00036"></a><span class="lineno">   36</span>&#160;<span class="preprocessor"></span><span class="preprocessor">#define OPENMS_TRANSFORMATIONS_FEATUREFINDER_FEATUREFINDERALGORITHMSIMPLE_H</span></div>
<div class="line"><a name="l00037"></a><span class="lineno">   37</span>&#160;<span class="preprocessor"></span></div>
<div class="line"><a name="l00038"></a><span class="lineno">   38</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="FeatureFinderAlgorithm_8h.html">OpenMS/TRANSFORMATIONS/FEATUREFINDER/FeatureFinderAlgorithm.h</a>&gt;</span></div>
<div class="line"><a name="l00039"></a><span class="lineno">   39</span>&#160;</div>
<div class="line"><a name="l00040"></a><span class="lineno">   40</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="SimpleSeeder_8h.html">OpenMS/TRANSFORMATIONS/FEATUREFINDER/SimpleSeeder.h</a>&gt;</span></div>
<div class="line"><a name="l00041"></a><span class="lineno">   41</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="SimpleExtender_8h.html">OpenMS/TRANSFORMATIONS/FEATUREFINDER/SimpleExtender.h</a>&gt;</span></div>
<div class="line"><a name="l00042"></a><span class="lineno">   42</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="ModelFitter_8h.html">OpenMS/TRANSFORMATIONS/FEATUREFINDER/ModelFitter.h</a>&gt;</span></div>
<div class="line"><a name="l00043"></a><span class="lineno">   43</span>&#160;</div>
<div class="line"><a name="l00044"></a><span class="lineno">   44</span>&#160;<span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00045"></a><span class="lineno">   45</span>&#160;{</div>
<div class="line"><a name="l00061"></a><span class="lineno">   61</span>&#160;  <span class="keyword">template</span> &lt;<span class="keyword">class</span> PeakType, <span class="keyword">class</span> FeatureType&gt;</div>
<div class="line"><a name="l00062"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmSimple.html">   62</a></span>&#160;  <span class="keyword">class </span><a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmSimple.html">FeatureFinderAlgorithmSimple</a> :</div>
<div class="line"><a name="l00063"></a><span class="lineno">   63</span>&#160;    <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html">FeatureFinderAlgorithm</a>&lt;PeakType, FeatureType&gt;,</div>
<div class="line"><a name="l00064"></a><span class="lineno">   64</span>&#160;    <span class="keyword">public</span> <a class="code" href="structOpenMS_1_1FeatureFinderDefs.html">FeatureFinderDefs</a></div>
<div class="line"><a name="l00065"></a><span class="lineno">   65</span>&#160;  {</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="keyword">public</span>:</div>
<div class="line"><a name="l00069"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmSimple.html#aa62472895cc326454e469c7a548560fe">   69</a></span>&#160;    <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmSimple.html#aa62472895cc326454e469c7a548560fe">FeatureFinderAlgorithmSimple</a>() :</div>
<div class="line"><a name="l00070"></a><span class="lineno">   70</span>&#160;      <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html">FeatureFinderAlgorithm</a>&lt;<a class="code" href="classOpenMS_1_1Peak2D.html">PeakType</a>, FeatureType&gt;()</div>
<div class="line"><a name="l00071"></a><span class="lineno">   71</span>&#160;    {</div>
<div class="line"><a name="l00072"></a><span class="lineno">   72</span>&#160;      this-&gt;<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a> = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmSimple.html#abe2fce5095efeecbcd815817430058e0">getDefaultParameters</a>();</div>
<div class="line"><a name="l00073"></a><span class="lineno">   73</span>&#160;      this-&gt;<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a7c3b265b697a57615da5cd3274780efd">check_defaults_</a> =  <span class="keyword">false</span>;</div>
<div class="line"><a name="l00074"></a><span class="lineno">   74</span>&#160;    }</div>
<div class="line"><a name="l00075"></a><span class="lineno">   75</span>&#160;</div>
<div class="line"><a name="l00076"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmSimple.html#abe2fce5095efeecbcd815817430058e0">   76</a></span>&#160;    <span class="keyword">virtual</span> <a class="code" href="classOpenMS_1_1Param.html">Param</a> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmSimple.html#abe2fce5095efeecbcd815817430058e0">getDefaultParameters</a>()<span class="keyword"> const</span></div>
<div class="line"><a name="l00077"></a><span class="lineno">   77</span>&#160;<span class="keyword">    </span>{</div>
<div class="line"><a name="l00078"></a><span class="lineno">   78</span>&#160;      <a class="code" href="classOpenMS_1_1Param.html">Param</a> tmp;</div>
<div class="line"><a name="l00079"></a><span class="lineno">   79</span>&#160;</div>
<div class="line"><a name="l00080"></a><span class="lineno">   80</span>&#160;      <a class="code" href="classOpenMS_1_1SimpleSeeder.html">SimpleSeeder&lt;PeakType, FeatureType&gt;</a> seeder(this-&gt;<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a365c5cf67d48519199fe00cb5688d628">map_</a>, this-&gt;<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a5f09052343ef99616ad653897841ce3e">features_</a>, this-&gt;<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#adf68cb378c76b322b2cc4dbb2c145a3e">ff_</a>);</div>
<div class="line"><a name="l00081"></a><span class="lineno">   81</span>&#160;      tmp.<a class="code" href="classOpenMS_1_1Param.html#ad2dc775a73f96e91dd97c61c39e4e7b8">insert</a>(<span class="stringliteral">&quot;seeder:&quot;</span>, seeder.<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a7f6aab5a7dfbdd1c062a4352a29361f3">getParameters</a>());</div>
<div class="line"><a name="l00082"></a><span class="lineno">   82</span>&#160;      tmp.<a class="code" href="classOpenMS_1_1Param.html#a7dae78ea20f5b33125f50c6ee27b1a60">setSectionDescription</a>(<span class="stringliteral">&quot;seeder&quot;</span>, <span class="stringliteral">&quot;Settings for the seeder (Determines potential feature regions)&quot;</span>);</div>
<div class="line"><a name="l00083"></a><span class="lineno">   83</span>&#160;</div>
<div class="line"><a name="l00084"></a><span class="lineno">   84</span>&#160;      <a class="code" href="classOpenMS_1_1SimpleExtender.html">SimpleExtender&lt;PeakType, FeatureType&gt;</a> extender(this-&gt;<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a365c5cf67d48519199fe00cb5688d628">map_</a>, this-&gt;<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a5f09052343ef99616ad653897841ce3e">features_</a>, this-&gt;<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#adf68cb378c76b322b2cc4dbb2c145a3e">ff_</a>);</div>
<div class="line"><a name="l00085"></a><span class="lineno">   85</span>&#160;      tmp.<a class="code" href="classOpenMS_1_1Param.html#ad2dc775a73f96e91dd97c61c39e4e7b8">insert</a>(<span class="stringliteral">&quot;extender:&quot;</span>, extender.<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a7f6aab5a7dfbdd1c062a4352a29361f3">getParameters</a>());</div>
<div class="line"><a name="l00086"></a><span class="lineno">   86</span>&#160;      tmp.<a class="code" href="classOpenMS_1_1Param.html#a7dae78ea20f5b33125f50c6ee27b1a60">setSectionDescription</a>(<span class="stringliteral">&quot;extender&quot;</span>, <span class="stringliteral">&quot;Settings for the extender (Collects all peaks belonging to a feature)&quot;</span>);</div>
<div class="line"><a name="l00087"></a><span class="lineno">   87</span>&#160;</div>
<div class="line"><a name="l00088"></a><span class="lineno">   88</span>&#160;      <a class="code" href="classOpenMS_1_1ModelFitter.html">ModelFitter&lt;PeakType, FeatureType&gt;</a> fitter(this-&gt;<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a365c5cf67d48519199fe00cb5688d628">map_</a>, this-&gt;<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a5f09052343ef99616ad653897841ce3e">features_</a>, this-&gt;<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#adf68cb378c76b322b2cc4dbb2c145a3e">ff_</a>);</div>
<div class="line"><a name="l00089"></a><span class="lineno">   89</span>&#160;      tmp.<a class="code" href="classOpenMS_1_1Param.html#ad2dc775a73f96e91dd97c61c39e4e7b8">insert</a>(<span class="stringliteral">&quot;fitter:&quot;</span>, fitter.<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a7f6aab5a7dfbdd1c062a4352a29361f3">getParameters</a>());</div>
<div class="line"><a name="l00090"></a><span class="lineno">   90</span>&#160;      tmp.<a class="code" href="classOpenMS_1_1Param.html#a7dae78ea20f5b33125f50c6ee27b1a60">setSectionDescription</a>(<span class="stringliteral">&quot;fitter&quot;</span>, <span class="stringliteral">&quot;Settings for the modefitter (Fits a model to the data determinging the probapility that they represent a feature.)&quot;</span>);</div>
<div class="line"><a name="l00091"></a><span class="lineno">   91</span>&#160;</div>
<div class="line"><a name="l00092"></a><span class="lineno">   92</span>&#160;      <span class="keywordflow">return</span> tmp;</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">   94</span>&#160;</div>
<div class="line"><a name="l00095"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmSimple.html#a72fcb26a14f6beb1c3fbace9ab3e7dbb">   95</a></span>&#160;    <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmSimple.html#a72fcb26a14f6beb1c3fbace9ab3e7dbb">run</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;<span class="preprocessor">#ifdef DEBUG_FEATUREFINDER</span></div>
<div class="line"><a name="l00098"></a><span class="lineno">   98</span>&#160;<span class="preprocessor"></span>      <a class="code" href="classunsigned_01int.html">UInt</a> seed_nr = 0;</div>
<div class="line"><a name="l00099"></a><span class="lineno">   99</span>&#160;<span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00100"></a><span class="lineno">  100</span>&#160;<span class="preprocessor"></span>      <a class="code" href="classOpenMS_1_1SimpleSeeder.html">SimpleSeeder&lt;PeakType, FeatureType&gt;</a> seeder(this-&gt;<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a365c5cf67d48519199fe00cb5688d628">map_</a>, this-&gt;<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a5f09052343ef99616ad653897841ce3e">features_</a>, this-&gt;<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#adf68cb378c76b322b2cc4dbb2c145a3e">ff_</a>);</div>
<div class="line"><a name="l00101"></a><span class="lineno">  101</span>&#160;      seeder.<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#abc8067511cfc949ae942ea2b08588f81">setParameters</a>(this-&gt;<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a7f6aab5a7dfbdd1c062a4352a29361f3">getParameters</a>().copy(<span class="stringliteral">&quot;seeder:&quot;</span>, <span class="keyword">true</span>));</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">  103</span>&#160;      <a class="code" href="classOpenMS_1_1SimpleExtender.html">SimpleExtender&lt;PeakType, FeatureType&gt;</a> extender(this-&gt;<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a365c5cf67d48519199fe00cb5688d628">map_</a>, this-&gt;<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a5f09052343ef99616ad653897841ce3e">features_</a>, this-&gt;<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#adf68cb378c76b322b2cc4dbb2c145a3e">ff_</a>);</div>
<div class="line"><a name="l00104"></a><span class="lineno">  104</span>&#160;      extender.<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#abc8067511cfc949ae942ea2b08588f81">setParameters</a>(this-&gt;<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a7f6aab5a7dfbdd1c062a4352a29361f3">getParameters</a>().copy(<span class="stringliteral">&quot;extender:&quot;</span>, <span class="keyword">true</span>));</div>
<div class="line"><a name="l00105"></a><span class="lineno">  105</span>&#160;</div>
<div class="line"><a name="l00106"></a><span class="lineno">  106</span>&#160;      <a class="code" href="classOpenMS_1_1ModelFitter.html">ModelFitter&lt;PeakType, FeatureType&gt;</a> fitter(this-&gt;<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a365c5cf67d48519199fe00cb5688d628">map_</a>, this-&gt;<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a5f09052343ef99616ad653897841ce3e">features_</a>, this-&gt;<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#adf68cb378c76b322b2cc4dbb2c145a3e">ff_</a>);</div>
<div class="line"><a name="l00107"></a><span class="lineno">  107</span>&#160;      <a class="code" href="classOpenMS_1_1Param.html">Param</a> params;</div>
<div class="line"><a name="l00108"></a><span class="lineno">  108</span>&#160;      params.<a class="code" href="classOpenMS_1_1Param.html#a33b2b89b6c31ab6fcf1e0babae08bd18">setDefaults</a>(this-&gt;<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a7f6aab5a7dfbdd1c062a4352a29361f3">getParameters</a>().copy(<span class="stringliteral">&quot;fitter:&quot;</span>, <span class="keyword">true</span>));</div>
<div class="line"><a name="l00109"></a><span class="lineno">  109</span>&#160;      params.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">&quot;fit_algorithm&quot;</span>, <span class="stringliteral">&quot;simple&quot;</span>);</div>
<div class="line"><a name="l00110"></a><span class="lineno">  110</span>&#160;      fitter.<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#abc8067511cfc949ae942ea2b08588f81">setParameters</a>(params);</div>
<div class="line"><a name="l00111"></a><span class="lineno">  111</span>&#160;</div>
<div class="line"><a name="l00113"></a><span class="lineno">  113</span>&#160;      <a class="code" href="structOpenMS_1_1Summary.html">Summary</a> summary;</div>
<div class="line"><a name="l00114"></a><span class="lineno">  114</span>&#160;</div>
<div class="line"><a name="l00115"></a><span class="lineno">  115</span>&#160;      <span class="keywordflow">try</span></div>
<div class="line"><a name="l00116"></a><span class="lineno">  116</span>&#160;      {</div>
<div class="line"><a name="l00117"></a><span class="lineno">  117</span>&#160;        <span class="keywordflow">for</span> (;; )</div>
<div class="line"><a name="l00118"></a><span class="lineno">  118</span>&#160;        {</div>
<div class="line"><a name="l00119"></a><span class="lineno">  119</span>&#160;<span class="preprocessor">#ifdef DEBUG_FEATUREFINDER</span></div>
<div class="line"><a name="l00120"></a><span class="lineno">  120</span>&#160;<span class="preprocessor"></span>          std::cout &lt;&lt; <span class="stringliteral">&quot;===============================&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a name="l00121"></a><span class="lineno">  121</span>&#160;          std::cout &lt;&lt; <span class="stringliteral">&quot;### Seeder (seed # &quot;</span> &lt;&lt; ++seed_nr &lt;&lt; <span class="stringliteral">&quot;)...&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a name="l00122"></a><span class="lineno">  122</span>&#160;<span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00123"></a><span class="lineno">  123</span>&#160;<span class="preprocessor"></span>          <a class="code" href="structOpenMS_1_1FeatureFinderDefs.html#aaee0bfd850887fdc58115cead9e9b8b9">IndexPair</a> seed = seeder.<a class="code" href="classOpenMS_1_1SimpleSeeder.html#a9101eb2633f34b26a1436b3d8e1e7522">nextSeed</a>();</div>
<div class="line"><a name="l00124"></a><span class="lineno">  124</span>&#160;</div>
<div class="line"><a name="l00125"></a><span class="lineno">  125</span>&#160;<span class="preprocessor">#ifdef DEBUG_FEATUREFINDER</span></div>
<div class="line"><a name="l00126"></a><span class="lineno">  126</span>&#160;<span class="preprocessor"></span>          std::cout &lt;&lt; <span class="stringliteral">&quot;seed ... &quot;</span> &lt;&lt; seed.first &lt;&lt; <span class="stringliteral">&quot; - &quot;</span> &lt;&lt; seed.second &lt;&lt; std::endl;</div>
<div class="line"><a name="l00127"></a><span class="lineno">  127</span>&#160;          std::cout &lt;&lt; <span class="stringliteral">&quot;### Extender...&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a name="l00128"></a><span class="lineno">  128</span>&#160;<span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00129"></a><span class="lineno">  129</span>&#160;<span class="preprocessor"></span>          <a class="code" href="structOpenMS_1_1IsotopeCluster_1_1ChargedIndexSet.html">ChargedIndexSet</a> index_set;</div>
<div class="line"><a name="l00130"></a><span class="lineno">  130</span>&#160;          index_set.insert(seed);</div>
<div class="line"><a name="l00131"></a><span class="lineno">  131</span>&#160;          <a class="code" href="structOpenMS_1_1IsotopeCluster_1_1ChargedIndexSet.html">ChargedIndexSet</a> region;</div>
<div class="line"><a name="l00132"></a><span class="lineno">  132</span>&#160;          extender.<a class="code" href="classOpenMS_1_1SimpleExtender.html#a1139a06b7cf1886d1977e5afcfddfea6">extend</a>(index_set, region);</div>
<div class="line"><a name="l00133"></a><span class="lineno">  133</span>&#160;</div>
<div class="line"><a name="l00134"></a><span class="lineno">  134</span>&#160;<span class="preprocessor">#ifdef DEBUG_FEATUREFINDER</span></div>
<div class="line"><a name="l00135"></a><span class="lineno">  135</span>&#160;<span class="preprocessor"></span>          std::cout &lt;&lt; <span class="stringliteral">&quot;### ModelFitter...&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a name="l00136"></a><span class="lineno">  136</span>&#160;<span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00137"></a><span class="lineno">  137</span>&#160;<span class="preprocessor"></span>          <span class="keywordflow">try</span></div>
<div class="line"><a name="l00138"></a><span class="lineno">  138</span>&#160;          {</div>
<div class="line"><a name="l00139"></a><span class="lineno">  139</span>&#160;            this-&gt;<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a5f09052343ef99616ad653897841ce3e">features_</a>-&gt;push_back(fitter.<a class="code" href="classOpenMS_1_1ModelFitter.html#a9a599157dfa0c832cf50f5596342c73e">fit</a>(region));</div>
<div class="line"><a name="l00140"></a><span class="lineno">  140</span>&#160;</div>
<div class="line"><a name="l00141"></a><span class="lineno">  141</span>&#160;            <span class="comment">// gather information for fitting summary</span></div>
<div class="line"><a name="l00142"></a><span class="lineno">  142</span>&#160;            {</div>
<div class="line"><a name="l00143"></a><span class="lineno">  143</span>&#160;              <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1Feature.html">Feature</a> &amp; f = this-&gt;<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a5f09052343ef99616ad653897841ce3e">features_</a>-&gt;back();</div>
<div class="line"><a name="l00144"></a><span class="lineno">  144</span>&#160;</div>
<div class="line"><a name="l00145"></a><span class="lineno">  145</span>&#160;              <span class="comment">// quality, correlation</span></div>
<div class="line"><a name="l00146"></a><span class="lineno">  146</span>&#160;              <a class="code" href="classdouble.html">DoubleReal</a> corr = f.<a class="code" href="classOpenMS_1_1Feature.html#a0adf747960bee685e34bfbbe57a7089b">getOverallQuality</a>();</div>
<div class="line"><a name="l00147"></a><span class="lineno">  147</span>&#160;              summary.<a class="code" href="structOpenMS_1_1Summary.html#a3358137d55fd95058116ee88f2663a88">corr_mean</a> += corr;</div>
<div class="line"><a name="l00148"></a><span class="lineno">  148</span>&#160;              <span class="keywordflow">if</span> (corr &lt; summary.<a class="code" href="structOpenMS_1_1Summary.html#a71cb946fce0c9a14ad9c16ce9b12478d">corr_min</a>) summary.<a class="code" href="structOpenMS_1_1Summary.html#a71cb946fce0c9a14ad9c16ce9b12478d">corr_min</a> = corr;</div>
<div class="line"><a name="l00149"></a><span class="lineno">  149</span>&#160;              <span class="keywordflow">if</span> (corr &gt; summary.<a class="code" href="structOpenMS_1_1Summary.html#ada49faa76fd89acdb868bdc7a6dee4f3">corr_max</a>) summary.<a class="code" href="structOpenMS_1_1Summary.html#ada49faa76fd89acdb868bdc7a6dee4f3">corr_max</a> = corr;</div>
<div class="line"><a name="l00150"></a><span class="lineno">  150</span>&#160;</div>
<div class="line"><a name="l00151"></a><span class="lineno">  151</span>&#160;              <span class="comment">// charge</span></div>
<div class="line"><a name="l00152"></a><span class="lineno">  152</span>&#160;              <a class="code" href="classunsigned_01int.html">UInt</a> ch = f.<a class="code" href="classOpenMS_1_1BaseFeature.html#ac80a487ac41c375532f8bff16871ae15">getCharge</a>();</div>
<div class="line"><a name="l00153"></a><span class="lineno">  153</span>&#160;              <span class="keywordflow">if</span> (ch &gt;= summary.<a class="code" href="structOpenMS_1_1Summary.html#a9b56db69bb4951352b93c88462ff1ebf">charge</a>.size())</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;                summary.<a class="code" href="structOpenMS_1_1Summary.html#a9b56db69bb4951352b93c88462ff1ebf">charge</a>.resize(ch + 1);</div>
<div class="line"><a name="l00156"></a><span class="lineno">  156</span>&#160;              }</div>
<div class="line"><a name="l00157"></a><span class="lineno">  157</span>&#160;              summary.<a class="code" href="structOpenMS_1_1Summary.html#a9b56db69bb4951352b93c88462ff1ebf">charge</a>[ch]++;</div>
<div class="line"><a name="l00158"></a><span class="lineno">  158</span>&#160;</div>
<div class="line"><a name="l00159"></a><span class="lineno">  159</span>&#160;              <span class="comment">// MZ model type</span></div>
<div class="line"><a name="l00160"></a><span class="lineno">  160</span>&#160;              <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1Param.html">Param</a> &amp; p = f.<a class="code" href="classOpenMS_1_1Feature.html#a94eabbe00bbab2a589688631c807005e">getModelDescription</a>().<a class="code" href="classOpenMS_1_1ModelDescription.html#a8183b5d5ad2dcdeabbc0ef3e40b99ec7">getParam</a>();</div>
<div class="line"><a name="l00161"></a><span class="lineno">  161</span>&#160;              ++summary.<a class="code" href="structOpenMS_1_1Summary.html#ab0eab2f15ba67b518f5f559aed34f033">mz_model</a>[p.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">&quot;MZ&quot;</span>)];</div>
<div class="line"><a name="l00162"></a><span class="lineno">  162</span>&#160;</div>
<div class="line"><a name="l00163"></a><span class="lineno">  163</span>&#160;              <span class="comment">// standard deviation of isotopic peaks</span></div>
<div class="line"><a name="l00164"></a><span class="lineno">  164</span>&#160;              <span class="keywordflow">if</span> (p.<a class="code" href="classOpenMS_1_1Param.html#a1228c6f4950f49a2f819b48db40ee071">exists</a>(<span class="stringliteral">&quot;MZ:isotope:stdev&quot;</span>) &amp;&amp; p.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">&quot;MZ:isotope:stdev&quot;</span>) != <a class="code" href="classOpenMS_1_1DataValue.html#a078588ac6fbb817e4d04ea210c86d323">DataValue::EMPTY</a>)</div>
<div class="line"><a name="l00165"></a><span class="lineno">  165</span>&#160;              {</div>
<div class="line"><a name="l00166"></a><span class="lineno">  166</span>&#160;                ++summary.<a class="code" href="structOpenMS_1_1Summary.html#a0e61382ce2ca1e403a6cf0a540a205af">mz_stdev</a>[p.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">&quot;MZ:isotope:stdev&quot;</span>)];</div>
<div class="line"><a name="l00167"></a><span class="lineno">  167</span>&#160;              }</div>
<div class="line"><a name="l00168"></a><span class="lineno">  168</span>&#160;            }</div>
<div class="line"><a name="l00169"></a><span class="lineno">  169</span>&#160;          }</div>
<div class="line"><a name="l00170"></a><span class="lineno">  170</span>&#160;          <span class="keywordflow">catch</span> (<a class="code" href="classOpenMS_1_1Exception_1_1UnableToFit.html">Exception::UnableToFit</a> ex)</div>
<div class="line"><a name="l00171"></a><span class="lineno">  171</span>&#160;          {</div>
<div class="line"><a name="l00172"></a><span class="lineno">  172</span>&#160;            <span class="comment">//std::cout &lt;&lt; &quot;UnableToFit: &quot; &lt;&lt; ex.what() &lt;&lt; std::endl;</span></div>
<div class="line"><a name="l00173"></a><span class="lineno">  173</span>&#160;</div>
<div class="line"><a name="l00174"></a><span class="lineno">  174</span>&#160;            <span class="comment">// set unused flag for all data points</span></div>
<div class="line"><a name="l00175"></a><span class="lineno">  175</span>&#160;            <span class="keywordflow">for</span> (IndexSet::const_iterator it = region.begin(); it != region.end(); ++it)</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;              this-&gt;<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#adf68cb378c76b322b2cc4dbb2c145a3e">ff_</a>-&gt;<a class="code" href="classOpenMS_1_1FeatureFinder.html#a91adbb58dfeb79d2b5d78c1047f406c9">getPeakFlag</a>(*it) = <a class="code" href="structOpenMS_1_1FeatureFinderDefs.html#a3f3de3e0d751949b8d0b60ffb302944aaa09b651ef326a9d8efcee5cc5b720ab4">UNUSED</a>;</div>
<div class="line"><a name="l00178"></a><span class="lineno">  178</span>&#160;            }</div>
<div class="line"><a name="l00179"></a><span class="lineno">  179</span>&#160;</div>
<div class="line"><a name="l00180"></a><span class="lineno">  180</span>&#160;            <span class="comment">// gather information for fitting summary</span></div>
<div class="line"><a name="l00181"></a><span class="lineno">  181</span>&#160;            {</div>
<div class="line"><a name="l00182"></a><span class="lineno">  182</span>&#160;              ++summary.<a class="code" href="structOpenMS_1_1Summary.html#ac68ce663c906bb967bc90b60c355d009">no_exceptions</a>;</div>
<div class="line"><a name="l00183"></a><span class="lineno">  183</span>&#160;              ++summary.<a class="code" href="structOpenMS_1_1Summary.html#a08ed2a5eb5d54783930d2b81ec1a54f3">exception</a>[ex.<a class="code" href="classOpenMS_1_1Exception_1_1BaseException.html#a2ad8ebd431528d7f92ce9a2fa14ccb34">getName</a>()];</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;          }</div>
<div class="line"><a name="l00186"></a><span class="lineno">  186</span>&#160;        }         <span class="comment">// for</span></div>
<div class="line"><a name="l00187"></a><span class="lineno">  187</span>&#160;      }       <span class="comment">// try</span></div>
<div class="line"><a name="l00188"></a><span class="lineno">  188</span>&#160;      <span class="keywordflow">catch</span> (<a class="code" href="classOpenMS_1_1FeatureFinderDefs_1_1NoSuccessor.html">NoSuccessor</a> ex)</div>
<div class="line"><a name="l00189"></a><span class="lineno">  189</span>&#160;      {</div>
<div class="line"><a name="l00190"></a><span class="lineno">  190</span>&#160;      }</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;      this-&gt;<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#adf68cb378c76b322b2cc4dbb2c145a3e">ff_</a>-&gt;<a class="code" href="classOpenMS_1_1ProgressLogger.html#a1cc1012b0cdaea97f58d571af1ff45de">endProgress</a>();</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;      <span class="comment">// print fitting summary</span></div>
<div class="line"><a name="l00195"></a><span class="lineno">  195</span>&#160;      {</div>
<div class="line"><a name="l00196"></a><span class="lineno">  196</span>&#160;        <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> size = this-&gt;<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a5f09052343ef99616ad653897841ce3e">features_</a>-&gt;size();</div>
<div class="line"><a name="l00197"></a><span class="lineno">  197</span>&#160;        std::cout &lt;&lt; size &lt;&lt; <span class="stringliteral">&quot; features were found. &quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a name="l00198"></a><span class="lineno">  198</span>&#160;</div>
<div class="line"><a name="l00199"></a><span class="lineno">  199</span>&#160;        <span class="comment">// compute corr_mean</span></div>
<div class="line"><a name="l00200"></a><span class="lineno">  200</span>&#160;        summary.<a class="code" href="structOpenMS_1_1Summary.html#a3358137d55fd95058116ee88f2663a88">corr_mean</a> /= size;</div>
<div class="line"><a name="l00201"></a><span class="lineno">  201</span>&#160;</div>
<div class="line"><a name="l00202"></a><span class="lineno">  202</span>&#160;        std::cout &lt;&lt; <span class="stringliteral">&quot;FeatureFinder summary:\n&quot;</span></div>
<div class="line"><a name="l00203"></a><span class="lineno">  203</span>&#160;                  &lt;&lt; <span class="stringliteral">&quot;Correlation:\n\tminimum: &quot;</span> &lt;&lt; summary.<a class="code" href="structOpenMS_1_1Summary.html#a71cb946fce0c9a14ad9c16ce9b12478d">corr_min</a> &lt;&lt; <span class="stringliteral">&quot;\n\tmean: &quot;</span> &lt;&lt; summary.<a class="code" href="structOpenMS_1_1Summary.html#a3358137d55fd95058116ee88f2663a88">corr_mean</a></div>
<div class="line"><a name="l00204"></a><span class="lineno">  204</span>&#160;                  &lt;&lt; <span class="stringliteral">&quot;\n\tmaximum: &quot;</span> &lt;&lt; summary.<a class="code" href="structOpenMS_1_1Summary.html#ada49faa76fd89acdb868bdc7a6dee4f3">corr_max</a> &lt;&lt; std::endl;</div>
<div class="line"><a name="l00205"></a><span class="lineno">  205</span>&#160;</div>
<div class="line"><a name="l00206"></a><span class="lineno">  206</span>&#160;        std::cout &lt;&lt; <span class="stringliteral">&quot;Exceptions:\n&quot;</span>;</div>
<div class="line"><a name="l00207"></a><span class="lineno">  207</span>&#160;        <span class="keywordflow">for</span> (std::map&lt;String, UInt&gt;::const_iterator it = summary.<a class="code" href="structOpenMS_1_1Summary.html#a08ed2a5eb5d54783930d2b81ec1a54f3">exception</a>.begin(); it != summary.<a class="code" href="structOpenMS_1_1Summary.html#a08ed2a5eb5d54783930d2b81ec1a54f3">exception</a>.end(); ++it)</div>
<div class="line"><a name="l00208"></a><span class="lineno">  208</span>&#160;        {</div>
<div class="line"><a name="l00209"></a><span class="lineno">  209</span>&#160;          std::cout &lt;&lt; <span class="stringliteral">&quot;\t&quot;</span> &lt;&lt; it-&gt;first &lt;&lt; <span class="stringliteral">&quot;: &quot;</span> &lt;&lt; it-&gt;second * 100 / summary.<a class="code" href="structOpenMS_1_1Summary.html#ac68ce663c906bb967bc90b60c355d009">no_exceptions</a> &lt;&lt; <span class="stringliteral">&quot;% (&quot;</span> &lt;&lt; it-&gt;second &lt;&lt; <span class="stringliteral">&quot;)\n&quot;</span>;</div>
<div class="line"><a name="l00210"></a><span class="lineno">  210</span>&#160;        }</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;        std::cout &lt;&lt; <span class="stringliteral">&quot;Chosen mz models:\n&quot;</span>;</div>
<div class="line"><a name="l00213"></a><span class="lineno">  213</span>&#160;        <span class="keywordflow">for</span> (std::map&lt;String, UInt&gt;::const_iterator it = summary.<a class="code" href="structOpenMS_1_1Summary.html#ab0eab2f15ba67b518f5f559aed34f033">mz_model</a>.begin(); it != summary.<a class="code" href="structOpenMS_1_1Summary.html#ab0eab2f15ba67b518f5f559aed34f033">mz_model</a>.end(); ++it)</div>
<div class="line"><a name="l00214"></a><span class="lineno">  214</span>&#160;        {</div>
<div class="line"><a name="l00215"></a><span class="lineno">  215</span>&#160;          std::cout &lt;&lt; <span class="stringliteral">&quot;\t&quot;</span> &lt;&lt; it-&gt;first &lt;&lt; <span class="stringliteral">&quot;: &quot;</span> &lt;&lt; it-&gt;second * 100 / size &lt;&lt; <span class="stringliteral">&quot;% (&quot;</span> &lt;&lt; it-&gt;second &lt;&lt; <span class="stringliteral">&quot;)\n&quot;</span>;</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;        std::cout &lt;&lt; <span class="stringliteral">&quot;Chosen mz stdevs:\n&quot;</span>;</div>
<div class="line"><a name="l00219"></a><span class="lineno">  219</span>&#160;        <span class="keywordflow">for</span> (std::map&lt;float, UInt&gt;::const_iterator it = summary.<a class="code" href="structOpenMS_1_1Summary.html#a0e61382ce2ca1e403a6cf0a540a205af">mz_stdev</a>.begin(); it != summary.<a class="code" href="structOpenMS_1_1Summary.html#a0e61382ce2ca1e403a6cf0a540a205af">mz_stdev</a>.end(); ++it)</div>
<div class="line"><a name="l00220"></a><span class="lineno">  220</span>&#160;        {</div>
<div class="line"><a name="l00221"></a><span class="lineno">  221</span>&#160;          std::cout &lt;&lt; <span class="stringliteral">&quot;\t&quot;</span> &lt;&lt; it-&gt;first &lt;&lt; <span class="stringliteral">&quot;: &quot;</span> &lt;&lt; it-&gt;second * 100 / (size - summary.<a class="code" href="structOpenMS_1_1Summary.html#a9b56db69bb4951352b93c88462ff1ebf">charge</a>[0]) &lt;&lt; <span class="stringliteral">&quot;% (&quot;</span> &lt;&lt; it-&gt;second &lt;&lt; <span class="stringliteral">&quot;)\n&quot;</span>;</div>
<div class="line"><a name="l00222"></a><span class="lineno">  222</span>&#160;        }</div>
<div class="line"><a name="l00223"></a><span class="lineno">  223</span>&#160;</div>
<div class="line"><a name="l00224"></a><span class="lineno">  224</span>&#160;        std::cout &lt;&lt; <span class="stringliteral">&quot;Charges:\n&quot;</span>;</div>
<div class="line"><a name="l00225"></a><span class="lineno">  225</span>&#160;        <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 1; i &lt; summary.<a class="code" href="structOpenMS_1_1Summary.html#a9b56db69bb4951352b93c88462ff1ebf">charge</a>.size(); ++i)</div>
<div class="line"><a name="l00226"></a><span class="lineno">  226</span>&#160;        {</div>
<div class="line"><a name="l00227"></a><span class="lineno">  227</span>&#160;          <span class="keywordflow">if</span> (summary.<a class="code" href="structOpenMS_1_1Summary.html#a9b56db69bb4951352b93c88462ff1ebf">charge</a>[i] != 0)</div>
<div class="line"><a name="l00228"></a><span class="lineno">  228</span>&#160;          {</div>
<div class="line"><a name="l00229"></a><span class="lineno">  229</span>&#160;            std::cout &lt;&lt; <span class="stringliteral">&quot;\t+&quot;</span> &lt;&lt; i &lt;&lt; <span class="stringliteral">&quot;: &quot;</span> &lt;&lt; summary.<a class="code" href="structOpenMS_1_1Summary.html#a9b56db69bb4951352b93c88462ff1ebf">charge</a>[i] * 100 / (size - summary.<a class="code" href="structOpenMS_1_1Summary.html#a9b56db69bb4951352b93c88462ff1ebf">charge</a>[0]) &lt;&lt; <span class="stringliteral">&quot;% (&quot;</span> &lt;&lt; summary.<a class="code" href="structOpenMS_1_1Summary.html#a9b56db69bb4951352b93c88462ff1ebf">charge</a>[i] &lt;&lt; <span class="stringliteral">&quot;)\n&quot;</span>;</div>
<div class="line"><a name="l00230"></a><span class="lineno">  230</span>&#160;          }</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;    }     <span class="comment">// run</span></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"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmSimple.html#a81483ea6deb5aa7b6e11d0c3c871f532">  235</a></span>&#160;    <span class="keyword">static</span> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html">FeatureFinderAlgorithm&lt;PeakType, FeatureType&gt;</a> * <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmSimple.html#a81483ea6deb5aa7b6e11d0c3c871f532">create</a>()</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;      <span class="keywordflow">return</span> <span class="keyword">new</span> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmSimple.html#aa62472895cc326454e469c7a548560fe">FeatureFinderAlgorithmSimple</a>();</div>
<div class="line"><a name="l00238"></a><span class="lineno">  238</span>&#160;    }</div>
<div class="line"><a name="l00239"></a><span class="lineno">  239</span>&#160;</div>
<div class="line"><a name="l00240"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmSimple.html#af73fd15708e50e77665070023a09cc87">  240</a></span>&#160;    <span class="keyword">static</span> <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmSimple.html#af73fd15708e50e77665070023a09cc87">getProductName</a>()</div>
<div class="line"><a name="l00241"></a><span class="lineno">  241</span>&#160;    {</div>
<div class="line"><a name="l00242"></a><span class="lineno">  242</span>&#160;      <span class="keywordflow">return</span> <span class="stringliteral">&quot;simple&quot;</span>;</div>
<div class="line"><a name="l00243"></a><span class="lineno">  243</span>&#160;    }</div>
<div class="line"><a name="l00244"></a><span class="lineno">  244</span>&#160;</div>
<div class="line"><a name="l00245"></a><span class="lineno">  245</span>&#160;<span class="keyword">private</span>:</div>
<div class="line"><a name="l00247"></a><span class="lineno">  247</span>&#160;    <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmSimple.html">FeatureFinderAlgorithmSimple</a> &amp; <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmSimple.html#aa57cbda803638f32d5a30800029f3d50">operator=</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmSimple.html">FeatureFinderAlgorithmSimple</a> &amp;);</div>
<div class="line"><a name="l00249"></a><span class="lineno">  249</span>&#160;    <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmSimple.html#aa62472895cc326454e469c7a548560fe">FeatureFinderAlgorithmSimple</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmSimple.html">FeatureFinderAlgorithmSimple</a> &amp;);</div>
<div class="line"><a name="l00250"></a><span class="lineno">  250</span>&#160;</div>
<div class="line"><a name="l00251"></a><span class="lineno">  251</span>&#160;  };   <span class="comment">// FeatureFinderAlgorithmSimple</span></div>
<div class="line"><a name="l00252"></a><span class="lineno">  252</span>&#160;</div>
<div class="line"><a name="l00253"></a><span class="lineno">  253</span>&#160;} <span class="comment">// namespace OpenMS</span></div>
<div class="line"><a name="l00254"></a><span class="lineno">  254</span>&#160;</div>
<div class="line"><a name="l00255"></a><span class="lineno">  255</span>&#160;<span class="preprocessor">#endif // OPENMS_TRANSFORMATIONS_FEATUREFINDER_FEATUREFINDERALGORITHMSIMPLE_H</span></div>
<div class="ttc" id="SimpleSeeder_8h_html"><div class="ttname"><a href="SimpleSeeder_8h.html">SimpleSeeder.h</a></div></div>
<div class="ttc" id="classunsigned_01int_html"><div class="ttname"><a href="classunsigned_01int.html">unsigned int</a></div></div>
<div class="ttc" id="structOpenMS_1_1Summary_html_ac68ce663c906bb967bc90b60c355d009"><div class="ttname"><a href="structOpenMS_1_1Summary.html#ac68ce663c906bb967bc90b60c355d009">OpenMS::Summary::no_exceptions</a></div><div class="ttdeci">UInt no_exceptions</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithm.h:53</div></div>
<div class="ttc" id="classOpenMS_1_1BaseFeature_html_ac80a487ac41c375532f8bff16871ae15"><div class="ttname"><a href="classOpenMS_1_1BaseFeature.html#ac80a487ac41c375532f8bff16871ae15">OpenMS::BaseFeature::getCharge</a></div><div class="ttdeci">const ChargeType &amp; getCharge() const </div><div class="ttdoc">Non-mutable access to charge state. </div></div>
<div class="ttc" id="classOpenMS_1_1SimpleExtender_html_a1139a06b7cf1886d1977e5afcfddfea6"><div class="ttname"><a href="classOpenMS_1_1SimpleExtender.html#a1139a06b7cf1886d1977e5afcfddfea6">OpenMS::SimpleExtender::extend</a></div><div class="ttdeci">void extend(const ChargedIndexSet &amp;seed_region, ChargedIndexSet &amp;result_region)</div><div class="ttdoc">return next seed </div><div class="ttdef"><b>Definition:</b> SimpleExtender.h:127</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmSimple_html_abe2fce5095efeecbcd815817430058e0"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmSimple.html#abe2fce5095efeecbcd815817430058e0">OpenMS::FeatureFinderAlgorithmSimple::getDefaultParameters</a></div><div class="ttdeci">virtual Param getDefaultParameters() const </div><div class="ttdoc">Returns the default parameters. Reimplment. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmSimple.h:76</div></div>
<div class="ttc" id="structOpenMS_1_1FeatureFinderDefs_html_aaee0bfd850887fdc58115cead9e9b8b9"><div class="ttname"><a href="structOpenMS_1_1FeatureFinderDefs.html#aaee0bfd850887fdc58115cead9e9b8b9">OpenMS::FeatureFinderDefs::IndexPair</a></div><div class="ttdeci">IsotopeCluster::IndexPair IndexPair</div><div class="ttdoc">Index to peak consisting of two UInts (scan index / peak index) </div><div class="ttdef"><b>Definition:</b> FeatureFinderDefs.h:54</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithm_html_a5f09052343ef99616ad653897841ce3e"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithm.html#a5f09052343ef99616ad653897841ce3e">OpenMS::FeatureFinderAlgorithm::features_</a></div><div class="ttdeci">FeatureMapType * features_</div><div class="ttdoc">Output data pointer. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithm.h:144</div></div>
<div class="ttc" id="classOpenMS_1_1DefaultParamHandler_html_a761b1937850c141d0c6fff0e4d633a04"><div class="ttname"><a href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">OpenMS::DefaultParamHandler::defaults_</a></div><div class="ttdeci">Param defaults_</div><div class="ttdoc">Container for default parameters. This member should be filled in the constructor of derived classes!...</div><div class="ttdef"><b>Definition:</b> DefaultParamHandler.h:155</div></div>
<div class="ttc" id="classOpenMS_1_1Param_html_a432099944e11263aa20aaf8ea1389790"><div class="ttname"><a href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">OpenMS::Param::setValue</a></div><div class="ttdeci">void setValue(const String &amp;key, const DataValue &amp;value, const String &amp;description=&quot;&quot;, const StringList &amp;tags=StringList())</div><div class="ttdoc">Sets a value. </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_1Feature_html_a94eabbe00bbab2a589688631c807005e"><div class="ttname"><a href="classOpenMS_1_1Feature.html#a94eabbe00bbab2a589688631c807005e">OpenMS::Feature::getModelDescription</a></div><div class="ttdeci">const ModelDescription&lt; 2 &gt; &amp; getModelDescription() const </div><div class="ttdoc">Non-mutable access to the model description. </div></div>
<div class="ttc" id="classOpenMS_1_1Param_html_ad2dc775a73f96e91dd97c61c39e4e7b8"><div class="ttname"><a href="classOpenMS_1_1Param.html#ad2dc775a73f96e91dd97c61c39e4e7b8">OpenMS::Param::insert</a></div><div class="ttdeci">void insert(const String &amp;prefix, const Param &amp;param)</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithm_html_adf68cb378c76b322b2cc4dbb2c145a3e"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithm.html#adf68cb378c76b322b2cc4dbb2c145a3e">OpenMS::FeatureFinderAlgorithm::ff_</a></div><div class="ttdeci">FeatureFinder * ff_</div><div class="ttdoc">Pointer to the calling FeatureFinder that is used to access the feature flags. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithm.h:147</div></div>
<div class="ttc" id="classOpenMS_1_1Peak2D_html"><div class="ttname"><a href="classOpenMS_1_1Peak2D.html">OpenMS::Peak2D</a></div><div class="ttdoc">A 2-dimensional raw data point or peak. </div><div class="ttdef"><b>Definition:</b> Peak2D.h:55</div></div>
<div class="ttc" id="classOpenMS_1_1Feature_html_a0adf747960bee685e34bfbbe57a7089b"><div class="ttname"><a href="classOpenMS_1_1Feature.html#a0adf747960bee685e34bfbbe57a7089b">OpenMS::Feature::getOverallQuality</a></div><div class="ttdeci">QualityType getOverallQuality() const </div><div class="ttdoc">Non-mutable access to the overall quality. </div></div>
<div class="ttc" id="structOpenMS_1_1FeatureFinderDefs_html_a3f3de3e0d751949b8d0b60ffb302944aaa09b651ef326a9d8efcee5cc5b720ab4"><div class="ttname"><a href="structOpenMS_1_1FeatureFinderDefs.html#a3f3de3e0d751949b8d0b60ffb302944aaa09b651ef326a9d8efcee5cc5b720ab4">OpenMS::FeatureFinderDefs::UNUSED</a></div><div class="ttdef"><b>Definition:</b> FeatureFinderDefs.h:63</div></div>
<div class="ttc" id="structOpenMS_1_1Summary_html_a3358137d55fd95058116ee88f2663a88"><div class="ttname"><a href="structOpenMS_1_1Summary.html#a3358137d55fd95058116ee88f2663a88">OpenMS::Summary::corr_mean</a></div><div class="ttdeci">DoubleReal corr_mean</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithm.h:57</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithm_html_a365c5cf67d48519199fe00cb5688d628"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithm.html#a365c5cf67d48519199fe00cb5688d628">OpenMS::FeatureFinderAlgorithm::map_</a></div><div class="ttdeci">const MapType * map_</div><div class="ttdoc">Input data pointer. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithm.h:141</div></div>
<div class="ttc" id="structOpenMS_1_1Summary_html_ab0eab2f15ba67b518f5f559aed34f033"><div class="ttname"><a href="structOpenMS_1_1Summary.html#ab0eab2f15ba67b518f5f559aed34f033">OpenMS::Summary::mz_model</a></div><div class="ttdeci">std::map&lt; String, UInt &gt; mz_model</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithm.h:54</div></div>
<div class="ttc" id="classOpenMS_1_1DataValue_html_a078588ac6fbb817e4d04ea210c86d323"><div class="ttname"><a href="classOpenMS_1_1DataValue.html#a078588ac6fbb817e4d04ea210c86d323">OpenMS::DataValue::EMPTY</a></div><div class="ttdeci">static const DataValue EMPTY</div><div class="ttdoc">Empty data value for comparisons. </div><div class="ttdef"><b>Definition:</b> DataValue.h:63</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithm_html"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithm.html">OpenMS::FeatureFinderAlgorithm</a></div><div class="ttdoc">Abstract base class for FeatureFinder algorithms. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithm.h:74</div></div>
<div class="ttc" id="classOpenMS_1_1Param_html_a7dae78ea20f5b33125f50c6ee27b1a60"><div class="ttname"><a href="classOpenMS_1_1Param.html#a7dae78ea20f5b33125f50c6ee27b1a60">OpenMS::Param::setSectionDescription</a></div><div class="ttdeci">void setSectionDescription(const String &amp;key, const String &amp;description)</div><div class="ttdoc">Sets a description for an existing section. </div></div>
<div class="ttc" id="classdouble_html"><div class="ttname"><a href="classdouble.html">double</a></div></div>
<div class="ttc" id="structOpenMS_1_1Summary_html_a0e61382ce2ca1e403a6cf0a540a205af"><div class="ttname"><a href="structOpenMS_1_1Summary.html#a0e61382ce2ca1e403a6cf0a540a205af">OpenMS::Summary::mz_stdev</a></div><div class="ttdeci">std::map&lt; float, UInt &gt; mz_stdev</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithm.h:55</div></div>
<div class="ttc" id="classOpenMS_1_1SimpleSeeder_html_a9101eb2633f34b26a1436b3d8e1e7522"><div class="ttname"><a href="classOpenMS_1_1SimpleSeeder.html#a9101eb2633f34b26a1436b3d8e1e7522">OpenMS::SimpleSeeder::nextSeed</a></div><div class="ttdeci">IndexPair nextSeed()</div><div class="ttdoc">return the next seed </div><div class="ttdef"><b>Definition:</b> SimpleSeeder.h:94</div></div>
<div class="ttc" id="classOpenMS_1_1DefaultParamHandler_html_abc8067511cfc949ae942ea2b08588f81"><div class="ttname"><a href="classOpenMS_1_1DefaultParamHandler.html#abc8067511cfc949ae942ea2b08588f81">OpenMS::DefaultParamHandler::setParameters</a></div><div class="ttdeci">void setParameters(const Param &amp;param)</div><div class="ttdoc">Sets the parameters. </div></div>
<div class="ttc" id="structOpenMS_1_1FeatureFinderDefs_html"><div class="ttname"><a href="structOpenMS_1_1FeatureFinderDefs.html">OpenMS::FeatureFinderDefs</a></div><div class="ttdoc">The purpose of this struct is to provide definitions of classes and typedefs which are used throughou...</div><div class="ttdef"><b>Definition:</b> FeatureFinderDefs.h:51</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmSimple_html_a81483ea6deb5aa7b6e11d0c3c871f532"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmSimple.html#a81483ea6deb5aa7b6e11d0c3c871f532">OpenMS::FeatureFinderAlgorithmSimple::create</a></div><div class="ttdeci">static FeatureFinderAlgorithm&lt; PeakType, FeatureType &gt; * create()</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmSimple.h:235</div></div>
<div class="ttc" id="structOpenMS_1_1Summary_html_ada49faa76fd89acdb868bdc7a6dee4f3"><div class="ttname"><a href="structOpenMS_1_1Summary.html#ada49faa76fd89acdb868bdc7a6dee4f3">OpenMS::Summary::corr_max</a></div><div class="ttdeci">DoubleReal corr_max</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithm.h:57</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmSimple_html_af73fd15708e50e77665070023a09cc87"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmSimple.html#af73fd15708e50e77665070023a09cc87">OpenMS::FeatureFinderAlgorithmSimple::getProductName</a></div><div class="ttdeci">static const String getProductName()</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmSimple.h:240</div></div>
<div class="ttc" id="classOpenMS_1_1ProgressLogger_html_a1cc1012b0cdaea97f58d571af1ff45de"><div class="ttname"><a href="classOpenMS_1_1ProgressLogger.html#a1cc1012b0cdaea97f58d571af1ff45de">OpenMS::ProgressLogger::endProgress</a></div><div class="ttdeci">void endProgress() const </div><div class="ttdoc">Ends the progress display. </div></div>
<div class="ttc" id="classOpenMS_1_1Param_html_abd0f5571675ec99e1aa647b39e2a8711"><div class="ttname"><a href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">OpenMS::Param::getValue</a></div><div class="ttdeci">const DataValue &amp; getValue(const String &amp;key) const </div><div class="ttdoc">Returns a value of a parameter. </div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmSimple_html"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmSimple.html">OpenMS::FeatureFinderAlgorithmSimple</a></div><div class="ttdoc">FeatureFinderAlgorithm implementation using the Simple* modules. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmSimple.h:62</div></div>
<div class="ttc" id="structOpenMS_1_1Summary_html_a08ed2a5eb5d54783930d2b81ec1a54f3"><div class="ttname"><a href="structOpenMS_1_1Summary.html#a08ed2a5eb5d54783930d2b81ec1a54f3">OpenMS::Summary::exception</a></div><div class="ttdeci">std::map&lt; String, UInt &gt; exception</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithm.h:52</div></div>
<div class="ttc" id="classOpenMS_1_1Exception_1_1BaseException_html_a2ad8ebd431528d7f92ce9a2fa14ccb34"><div class="ttname"><a href="classOpenMS_1_1Exception_1_1BaseException.html#a2ad8ebd431528d7f92ce9a2fa14ccb34">OpenMS::Exception::BaseException::getName</a></div><div class="ttdeci">const char * getName() const </div><div class="ttdoc">Returns the name of the exception. </div></div>
<div class="ttc" id="classOpenMS_1_1Param_html_a33b2b89b6c31ab6fcf1e0babae08bd18"><div class="ttname"><a href="classOpenMS_1_1Param.html#a33b2b89b6c31ab6fcf1e0babae08bd18">OpenMS::Param::setDefaults</a></div><div class="ttdeci">void setDefaults(const Param &amp;defaults, const String &amp;prefix=&quot;&quot;, bool showMessage=false)</div><div class="ttdoc">Insert all values of defaults and adds the prefix prefix, if the values are not already set...</div></div>
<div class="ttc" id="structOpenMS_1_1Summary_html_a9b56db69bb4951352b93c88462ff1ebf"><div class="ttname"><a href="structOpenMS_1_1Summary.html#a9b56db69bb4951352b93c88462ff1ebf">OpenMS::Summary::charge</a></div><div class="ttdeci">std::vector&lt; UInt &gt; charge</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithm.h:56</div></div>
<div class="ttc" id="structOpenMS_1_1Summary_html"><div class="ttname"><a href="structOpenMS_1_1Summary.html">OpenMS::Summary</a></div><div class="ttdoc">Summary of fitting results. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithm.h:50</div></div>
<div class="ttc" id="classOpenMS_1_1SimpleExtender_html"><div class="ttname"><a href="classOpenMS_1_1SimpleExtender.html">OpenMS::SimpleExtender</a></div><div class="ttdoc">Simple feature extension algorithm. </div><div class="ttdef"><b>Definition:</b> SimpleExtender.h:79</div></div>
<div class="ttc" id="ModelFitter_8h_html"><div class="ttname"><a href="ModelFitter_8h.html">ModelFitter.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1ModelFitter_html"><div class="ttname"><a href="classOpenMS_1_1ModelFitter.html">OpenMS::ModelFitter</a></div><div class="ttdoc">Tests a group of data points in an LC-MS map for goodness-of-fit with a 2D averagine model...</div><div class="ttdef"><b>Definition:</b> ModelFitter.h:77</div></div>
<div class="ttc" id="classOpenMS_1_1Param_html_a1228c6f4950f49a2f819b48db40ee071"><div class="ttname"><a href="classOpenMS_1_1Param.html#a1228c6f4950f49a2f819b48db40ee071">OpenMS::Param::exists</a></div><div class="ttdeci">bool exists(const String &amp;key) const </div><div class="ttdoc">Tests if a parameter is set (expecting its fully qualified name, e.g., TextExporter:1:proteins_only) ...</div></div>
<div class="ttc" id="FeatureFinderAlgorithm_8h_html"><div class="ttname"><a href="FeatureFinderAlgorithm_8h.html">FeatureFinderAlgorithm.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderDefs_1_1NoSuccessor_html"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderDefs_1_1NoSuccessor.html">OpenMS::FeatureFinderDefs::NoSuccessor</a></div><div class="ttdoc">Exception that is thrown if a method an invalid IndexPair is given. </div><div class="ttdef"><b>Definition:</b> FeatureFinderDefs.h:66</div></div>
<div class="ttc" id="classOpenMS_1_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_1FeatureFinderAlgorithmSimple_html_aa62472895cc326454e469c7a548560fe"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmSimple.html#aa62472895cc326454e469c7a548560fe">OpenMS::FeatureFinderAlgorithmSimple::FeatureFinderAlgorithmSimple</a></div><div class="ttdeci">FeatureFinderAlgorithmSimple()</div><div class="ttdoc">default constructor </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmSimple.h:69</div></div>
<div class="ttc" id="classOpenMS_1_1Param_html"><div class="ttname"><a href="classOpenMS_1_1Param.html">OpenMS::Param</a></div><div class="ttdoc">Management and storage of parameters / INI files. </div><div class="ttdef"><b>Definition:</b> Param.h:69</div></div>
<div class="ttc" id="structOpenMS_1_1Summary_html_a71cb946fce0c9a14ad9c16ce9b12478d"><div class="ttname"><a href="structOpenMS_1_1Summary.html#a71cb946fce0c9a14ad9c16ce9b12478d">OpenMS::Summary::corr_min</a></div><div class="ttdeci">DoubleReal corr_min</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithm.h:57</div></div>
<div class="ttc" id="classOpenMS_1_1Exception_1_1UnableToFit_html"><div class="ttname"><a href="classOpenMS_1_1Exception_1_1UnableToFit.html">OpenMS::Exception::UnableToFit</a></div><div class="ttdoc">Exception used if an error occurred while fitting a model to a given dataset. </div><div class="ttdef"><b>Definition:</b> Exception.h:662</div></div>
<div class="ttc" id="structOpenMS_1_1IsotopeCluster_1_1ChargedIndexSet_html"><div class="ttname"><a href="structOpenMS_1_1IsotopeCluster_1_1ChargedIndexSet.html">OpenMS::IsotopeCluster::ChargedIndexSet</a></div><div class="ttdoc">index set with associated charge estimate </div><div class="ttdef"><b>Definition:</b> IsotopeCluster.h:53</div></div>
<div class="ttc" id="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_1ModelDescription_html_a8183b5d5ad2dcdeabbc0ef3e40b99ec7"><div class="ttname"><a href="classOpenMS_1_1ModelDescription.html#a8183b5d5ad2dcdeabbc0ef3e40b99ec7">OpenMS::ModelDescription::getParam</a></div><div class="ttdeci">const Param &amp; getParam() const </div><div class="ttdoc">Non-mutable access to model parameters. </div><div class="ttdef"><b>Definition:</b> ModelDescription.h:127</div></div>
<div class="ttc" id="classOpenMS_1_1DefaultParamHandler_html_a7c3b265b697a57615da5cd3274780efd"><div class="ttname"><a href="classOpenMS_1_1DefaultParamHandler.html#a7c3b265b697a57615da5cd3274780efd">OpenMS::DefaultParamHandler::check_defaults_</a></div><div class="ttdeci">bool check_defaults_</div><div class="ttdoc">If this member is set to false no checking if parameters in done;. </div><div class="ttdef"><b>Definition:</b> DefaultParamHandler.h:174</div></div>
<div class="ttc" id="SimpleExtender_8h_html"><div class="ttname"><a href="SimpleExtender_8h.html">SimpleExtender.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinder_html_a91adbb58dfeb79d2b5d78c1047f406c9"><div class="ttname"><a href="classOpenMS_1_1FeatureFinder.html#a91adbb58dfeb79d2b5d78c1047f406c9">OpenMS::FeatureFinder::getPeakFlag</a></div><div class="ttdeci">const Flag &amp; getPeakFlag(const IndexPair &amp;index) const </div><div class="ttdoc">Returns a non-mutable reference to a peak flag. </div><div class="ttdef"><b>Definition:</b> FeatureFinder.h:91</div></div>
<div class="ttc" id="classOpenMS_1_1SimpleSeeder_html"><div class="ttname"><a href="classOpenMS_1_1SimpleSeeder.html">OpenMS::SimpleSeeder</a></div><div class="ttdoc">Simple seeding class that uses the strongest peak as next seed. </div><div class="ttdef"><b>Definition:</b> SimpleSeeder.h:61</div></div>
<div class="ttc" id="classOpenMS_1_1ModelFitter_html_a9a599157dfa0c832cf50f5596342c73e"><div class="ttname"><a href="classOpenMS_1_1ModelFitter.html#a9a599157dfa0c832cf50f5596342c73e">OpenMS::ModelFitter::fit</a></div><div class="ttdeci">Feature fit(const ChargedIndexSet &amp;index_set)</div><div class="ttdoc">Return next feature. </div><div class="ttdef"><b>Definition:</b> ModelFitter.h:226</div></div>
<div class="ttc" id="classOpenMS_1_1DefaultParamHandler_html_a7f6aab5a7dfbdd1c062a4352a29361f3"><div class="ttname"><a href="classOpenMS_1_1DefaultParamHandler.html#a7f6aab5a7dfbdd1c062a4352a29361f3">OpenMS::DefaultParamHandler::getParameters</a></div><div class="ttdeci">const Param &amp; getParameters() const </div><div class="ttdoc">Non-mutable access to the parameters. </div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmSimple_html_aa57cbda803638f32d5a30800029f3d50"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmSimple.html#aa57cbda803638f32d5a30800029f3d50">OpenMS::FeatureFinderAlgorithmSimple::operator=</a></div><div class="ttdeci">FeatureFinderAlgorithmSimple &amp; operator=(const FeatureFinderAlgorithmSimple &amp;)</div><div class="ttdoc">Not implemented. </div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmSimple_html_a72fcb26a14f6beb1c3fbace9ab3e7dbb"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmSimple.html#a72fcb26a14f6beb1c3fbace9ab3e7dbb">OpenMS::FeatureFinderAlgorithmSimple::run</a></div><div class="ttdeci">virtual void run()</div><div class="ttdoc">Main method that implements the actual algorithm. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmSimple.h:95</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 11:19:13 using doxygen 1.8.5</font></TD>
</TR>
</TABLE>
</BODY>
</HTML>