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
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
|
<HTML>
<HEAD>
<TITLE>FeaFiModule.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> ·
<A href="classes.html">Classes</A> ·
<A href="annotated.html">Annotated Classes</A> ·
<A href="modules.html">Modules</A> ·
<A href="functions_func.html">Members</A> ·
<A href="namespaces.html">Namespaces</A> ·
<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">FeaFiModule.h</div> </div>
</div><!--header-->
<div class="contents">
<a href="FeaFiModule_8h.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="comment">// OpenMS -- Open-Source Mass Spectrometry</span></div>
<div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="comment">// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,</span></div>
<div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="comment">// ETH Zurich, and Freie Universitaet Berlin 2002-2013.</span></div>
<div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="comment">//</span></div>
<div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="comment">// This software is released under a three-clause BSD license:</span></div>
<div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="comment">// * Redistributions of source code must retain the above copyright</span></div>
<div class="line"><a name="l00009"></a><span class="lineno"> 9</span> <span class="comment">// notice, this list of conditions and the following disclaimer.</span></div>
<div class="line"><a name="l00010"></a><span class="lineno"> 10</span> <span class="comment">// * Redistributions in binary form must reproduce the above copyright</span></div>
<div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="comment">// notice, this list of conditions and the following disclaimer in the</span></div>
<div class="line"><a name="l00012"></a><span class="lineno"> 12</span> <span class="comment">// documentation and/or other materials provided with the distribution.</span></div>
<div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="comment">// * Neither the name of any author or any participating institution</span></div>
<div class="line"><a name="l00014"></a><span class="lineno"> 14</span> <span class="comment">// may be used to endorse or promote products derived from this software</span></div>
<div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="comment">// without specific prior written permission.</span></div>
<div class="line"><a name="l00016"></a><span class="lineno"> 16</span> <span class="comment">// For a full list of authors, refer to the file AUTHORS.</span></div>
<div class="line"><a name="l00017"></a><span class="lineno"> 17</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00018"></a><span class="lineno"> 18</span> <span class="comment">// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"</span></div>
<div class="line"><a name="l00019"></a><span class="lineno"> 19</span> <span class="comment">// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE</span></div>
<div class="line"><a name="l00020"></a><span class="lineno"> 20</span> <span class="comment">// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE</span></div>
<div class="line"><a name="l00021"></a><span class="lineno"> 21</span> <span class="comment">// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING</span></div>
<div class="line"><a name="l00022"></a><span class="lineno"> 22</span> <span class="comment">// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,</span></div>
<div class="line"><a name="l00023"></a><span class="lineno"> 23</span> <span class="comment">// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,</span></div>
<div class="line"><a name="l00024"></a><span class="lineno"> 24</span> <span class="comment">// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;</span></div>
<div class="line"><a name="l00025"></a><span class="lineno"> 25</span> <span class="comment">// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,</span></div>
<div class="line"><a name="l00026"></a><span class="lineno"> 26</span> <span class="comment">// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR</span></div>
<div class="line"><a name="l00027"></a><span class="lineno"> 27</span> <span class="comment">// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF</span></div>
<div class="line"><a name="l00028"></a><span class="lineno"> 28</span> <span class="comment">// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</span></div>
<div class="line"><a name="l00029"></a><span class="lineno"> 29</span> <span class="comment">//</span></div>
<div class="line"><a name="l00030"></a><span class="lineno"> 30</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00031"></a><span class="lineno"> 31</span> <span class="comment">// $Maintainer: Clemens Groepl $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno"> 32</span> <span class="comment">// $Authors: Marc Sturm, Clemens Groepl $</span></div>
<div class="line"><a name="l00033"></a><span class="lineno"> 33</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00034"></a><span class="lineno"> 34</span> </div>
<div class="line"><a name="l00035"></a><span class="lineno"> 35</span> <span class="preprocessor">#ifndef OPENMS_TRANSFORMATIONS_FEATUREFINDER_FEAFIMODULE_H</span></div>
<div class="line"><a name="l00036"></a><span class="lineno"> 36</span> <span class="preprocessor"></span><span class="preprocessor">#define OPENMS_TRANSFORMATIONS_FEATUREFINDER_FEAFIMODULE_H</span></div>
<div class="line"><a name="l00037"></a><span class="lineno"> 37</span> <span class="preprocessor"></span></div>
<div class="line"><a name="l00038"></a><span class="lineno"> 38</span> <span class="preprocessor">#include <<a class="code" href="DefaultParamHandler_8h.html">OpenMS/DATASTRUCTURES/DefaultParamHandler.h</a>></span></div>
<div class="line"><a name="l00039"></a><span class="lineno"> 39</span> <span class="preprocessor">#include <<a class="code" href="FeatureFinderDefs_8h.html">OpenMS/TRANSFORMATIONS/FEATUREFINDER/FeatureFinderDefs.h</a>></span></div>
<div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="preprocessor">#include <<a class="code" href="FeatureMap_8h.html">OpenMS/KERNEL/FeatureMap.h</a>></span></div>
<div class="line"><a name="l00041"></a><span class="lineno"> 41</span> <span class="preprocessor">#include <<a class="code" href="MSExperiment_8h.html">OpenMS/KERNEL/MSExperiment.h</a>></span></div>
<div class="line"><a name="l00042"></a><span class="lineno"> 42</span> </div>
<div class="line"><a name="l00043"></a><span class="lineno"> 43</span> <span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00044"></a><span class="lineno"> 44</span> {</div>
<div class="line"><a name="l00045"></a><span class="lineno"> 45</span> </div>
<div class="line"><a name="l00046"></a><span class="lineno"> 46</span>  <span class="keyword">class </span>FeatureFinder;</div>
<div class="line"><a name="l00047"></a><span class="lineno"> 47</span> </div>
<div class="line"><a name="l00048"></a><span class="lineno"> 48</span>  <span class="keyword">namespace </span>Internal</div>
<div class="line"><a name="l00049"></a><span class="lineno"> 49</span>  {</div>
<div class="line"><a name="l00050"></a><span class="lineno"> 50</span>  <span class="comment">//-------------------------------------------------------------------</span></div>
<div class="line"><a name="l00051"></a><span class="lineno"> 51</span> </div>
<div class="line"><a name="l00055"></a><span class="lineno"> 55</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> FeaFiModuleType></div>
<div class="line"><a name="l00056"></a><span class="lineno"><a class="line" href="structOpenMS_1_1Internal_1_1IntensityLess.html"> 56</a></span>  <span class="keyword">struct </span><a class="code" href="structOpenMS_1_1Internal_1_1IntensityLess.html">IntensityLess</a> :</div>
<div class="line"><a name="l00057"></a><span class="lineno"> 57</span>  std::binary_function<typename FeatureFinderDefs::IndexPair, typename FeatureFinderDefs::IndexPair, bool></div>
<div class="line"><a name="l00058"></a><span class="lineno"> 58</span>  {</div>
<div class="line"><a name="l00060"></a><span class="lineno"><a class="line" href="structOpenMS_1_1Internal_1_1IntensityLess.html#a30c8699daaee3f695c0f7736e50b4829"> 60</a></span>  <a class="code" href="structOpenMS_1_1Internal_1_1IntensityLess.html#a30c8699daaee3f695c0f7736e50b4829">IntensityLess</a>(<span class="keyword">const</span> FeaFiModuleType & module) :</div>
<div class="line"><a name="l00061"></a><span class="lineno"> 61</span>  <a class="code" href="structOpenMS_1_1Internal_1_1IntensityLess.html#a414b3def0d80594ea23bda8b4cd88b30">module_</a>(module)</div>
<div class="line"><a name="l00062"></a><span class="lineno"> 62</span>  {</div>
<div class="line"><a name="l00063"></a><span class="lineno"> 63</span>  }</div>
<div class="line"><a name="l00064"></a><span class="lineno"> 64</span> </div>
<div class="line"><a name="l00066"></a><span class="lineno"><a class="line" href="structOpenMS_1_1Internal_1_1IntensityLess.html#a6a3e75b9d7ab0a2dca8122e197b7fe5e"> 66</a></span>  <a class="code" href="structOpenMS_1_1Internal_1_1IntensityLess.html#a6a3e75b9d7ab0a2dca8122e197b7fe5e">IntensityLess</a>(<span class="keyword">const</span> <a class="code" href="structOpenMS_1_1Internal_1_1IntensityLess.html">IntensityLess</a> & rhs) :</div>
<div class="line"><a name="l00067"></a><span class="lineno"> 67</span>  <a class="code" href="structOpenMS_1_1Internal_1_1IntensityLess.html#a414b3def0d80594ea23bda8b4cd88b30">module_</a>(rhs.<a class="code" href="structOpenMS_1_1Internal_1_1IntensityLess.html#a414b3def0d80594ea23bda8b4cd88b30">module_</a>)</div>
<div class="line"><a name="l00068"></a><span class="lineno"> 68</span>  {</div>
<div class="line"><a name="l00069"></a><span class="lineno"> 69</span>  }</div>
<div class="line"><a name="l00070"></a><span class="lineno"> 70</span> </div>
<div class="line"><a name="l00072"></a><span class="lineno"><a class="line" href="structOpenMS_1_1Internal_1_1IntensityLess.html#a9baf7271d6c179b931d60d9f96e9e215"> 72</a></span>  <span class="keyword">inline</span> <span class="keywordtype">bool</span> <a class="code" href="structOpenMS_1_1Internal_1_1IntensityLess.html#a9baf7271d6c179b931d60d9f96e9e215">operator()</a>(<span class="keyword">const</span> <span class="keyword">typename</span> <a class="code" href="structOpenMS_1_1FeatureFinderDefs.html#aaee0bfd850887fdc58115cead9e9b8b9">FeatureFinderDefs::IndexPair</a> & left, <span class="keyword">const</span> <span class="keyword">typename</span> <a class="code" href="structOpenMS_1_1FeatureFinderDefs.html#aaee0bfd850887fdc58115cead9e9b8b9">FeatureFinderDefs::IndexPair</a> & right)<span class="keyword"> const</span></div>
<div class="line"><a name="l00073"></a><span class="lineno"> 73</span> <span class="keyword"> </span>{</div>
<div class="line"><a name="l00074"></a><span class="lineno"> 74</span>  <span class="keywordflow">return</span> <a class="code" href="structOpenMS_1_1Internal_1_1IntensityLess.html#a414b3def0d80594ea23bda8b4cd88b30">module_</a>.getPeakIntensity(left) < <a class="code" href="structOpenMS_1_1Internal_1_1IntensityLess.html#a414b3def0d80594ea23bda8b4cd88b30">module_</a>.getPeakIntensity(right);</div>
<div class="line"><a name="l00075"></a><span class="lineno"> 75</span>  }</div>
<div class="line"><a name="l00076"></a><span class="lineno"> 76</span> </div>
<div class="line"><a name="l00077"></a><span class="lineno"> 77</span> <span class="keyword">private</span>:</div>
<div class="line"><a name="l00079"></a><span class="lineno"><a class="line" href="structOpenMS_1_1Internal_1_1IntensityLess.html#a414b3def0d80594ea23bda8b4cd88b30"> 79</a></span>  <span class="keyword">const</span> FeaFiModuleType & <a class="code" href="structOpenMS_1_1Internal_1_1IntensityLess.html#a414b3def0d80594ea23bda8b4cd88b30">module_</a>;</div>
<div class="line"><a name="l00081"></a><span class="lineno"> 81</span>  <a class="code" href="structOpenMS_1_1Internal_1_1IntensityLess.html#a35b8d10c84a677edb9fbd6de39f21c7b">IntensityLess</a>();</div>
<div class="line"><a name="l00082"></a><span class="lineno"> 82</span>  }; <span class="comment">// struct IntensityLess</span></div>
<div class="line"><a name="l00083"></a><span class="lineno"> 83</span> </div>
<div class="line"><a name="l00084"></a><span class="lineno"> 84</span>  <span class="comment">//-------------------------------------------------------------------</span></div>
<div class="line"><a name="l00085"></a><span class="lineno"> 85</span> </div>
<div class="line"><a name="l00087"></a><span class="lineno"> 87</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> FeaFiModuleType></div>
<div class="line"><a name="l00088"></a><span class="lineno"><a class="line" href="structOpenMS_1_1Internal_1_1IntensityIterator.html"> 88</a></span>  <span class="keyword">struct </span><a class="code" href="structOpenMS_1_1Internal_1_1IntensityIterator.html">IntensityIterator</a> :</div>
<div class="line"><a name="l00089"></a><span class="lineno"> 89</span>  FeatureFinderDefs::IndexSet::const_iterator</div>
<div class="line"><a name="l00090"></a><span class="lineno"> 90</span>  {</div>
<div class="line"><a name="l00091"></a><span class="lineno"><a class="line" href="structOpenMS_1_1Internal_1_1IntensityIterator.html#aa3fbcf8848df3dc4e06c441ef10b4de4"> 91</a></span>  <a class="code" href="structOpenMS_1_1Internal_1_1IntensityIterator.html#aa3fbcf8848df3dc4e06c441ef10b4de4">IntensityIterator</a>(<span class="keyword">const</span> FeatureFinderDefs::IndexSet::const_iterator & iter, <span class="keyword">const</span> FeaFiModuleType * module) :</div>
<div class="line"><a name="l00092"></a><span class="lineno"> 92</span>  <a class="code" href="structOpenMS_1_1FeatureFinderDefs.html">FeatureFinderDefs</a>::IndexSet::const_iterator(iter),</div>
<div class="line"><a name="l00093"></a><span class="lineno"> 93</span>  <a class="code" href="structOpenMS_1_1Internal_1_1IntensityIterator.html#a3a08b12523ea66ba7871e9bc5c6ce1b0">module_</a>(module)</div>
<div class="line"><a name="l00094"></a><span class="lineno"> 94</span>  {</div>
<div class="line"><a name="l00095"></a><span class="lineno"> 95</span>  }</div>
<div class="line"><a name="l00096"></a><span class="lineno"> 96</span> </div>
<div class="line"><a name="l00097"></a><span class="lineno"><a class="line" href="structOpenMS_1_1Internal_1_1IntensityIterator.html#aa9d1657a3991181d4328f63df98fae1a"> 97</a></span>  <span class="keyword">typename</span> FeaFiModuleType::IntensityType <a class="code" href="structOpenMS_1_1Internal_1_1IntensityIterator.html#aa9d1657a3991181d4328f63df98fae1a">operator*</a>()<span class="keyword"> const</span></div>
<div class="line"><a name="l00098"></a><span class="lineno"> 98</span> <span class="keyword"> </span>{</div>
<div class="line"><a name="l00099"></a><span class="lineno"> 99</span>  <span class="keywordflow">return</span> <a class="code" href="structOpenMS_1_1Internal_1_1IntensityIterator.html#a3a08b12523ea66ba7871e9bc5c6ce1b0">module_</a>->getPeakIntensity(FeatureFinderDefs::IndexSet::const_iterator::operator*());</div>
<div class="line"><a name="l00100"></a><span class="lineno"> 100</span>  }</div>
<div class="line"><a name="l00101"></a><span class="lineno"> 101</span> </div>
<div class="line"><a name="l00102"></a><span class="lineno"> 102</span> <span class="keyword">protected</span>:</div>
<div class="line"><a name="l00103"></a><span class="lineno"><a class="line" href="structOpenMS_1_1Internal_1_1IntensityIterator.html#a3a08b12523ea66ba7871e9bc5c6ce1b0"> 103</a></span>  <span class="keyword">const</span> FeaFiModuleType * <a class="code" href="structOpenMS_1_1Internal_1_1IntensityIterator.html#a3a08b12523ea66ba7871e9bc5c6ce1b0">module_</a>;</div>
<div class="line"><a name="l00104"></a><span class="lineno"> 104</span>  };</div>
<div class="line"><a name="l00105"></a><span class="lineno"> 105</span> </div>
<div class="line"><a name="l00106"></a><span class="lineno"> 106</span>  <span class="comment">//-------------------------------------------------------------------</span></div>
<div class="line"><a name="l00107"></a><span class="lineno"> 107</span> </div>
<div class="line"><a name="l00109"></a><span class="lineno"> 109</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> FeaFiModuleType></div>
<div class="line"><a name="l00110"></a><span class="lineno"><a class="line" href="structOpenMS_1_1Internal_1_1MzIterator.html"> 110</a></span>  <span class="keyword">struct </span><a class="code" href="structOpenMS_1_1Internal_1_1MzIterator.html">MzIterator</a> :</div>
<div class="line"><a name="l00111"></a><span class="lineno"> 111</span>  FeatureFinderDefs::IndexSet::const_iterator</div>
<div class="line"><a name="l00112"></a><span class="lineno"> 112</span>  {</div>
<div class="line"><a name="l00113"></a><span class="lineno"><a class="line" href="structOpenMS_1_1Internal_1_1MzIterator.html#a5fa88c983f41e3ae1a39a41771f2daa2"> 113</a></span>  <a class="code" href="structOpenMS_1_1Internal_1_1MzIterator.html#a5fa88c983f41e3ae1a39a41771f2daa2">MzIterator</a>(<span class="keyword">const</span> FeatureFinderDefs::IndexSet::const_iterator & iter, <span class="keyword">const</span> FeaFiModuleType * module) :</div>
<div class="line"><a name="l00114"></a><span class="lineno"> 114</span>  <a class="code" href="structOpenMS_1_1FeatureFinderDefs.html">FeatureFinderDefs</a>::IndexSet::const_iterator(iter),</div>
<div class="line"><a name="l00115"></a><span class="lineno"> 115</span>  <a class="code" href="structOpenMS_1_1Internal_1_1MzIterator.html#a3a08b12523ea66ba7871e9bc5c6ce1b0">module_</a>(module)</div>
<div class="line"><a name="l00116"></a><span class="lineno"> 116</span>  {</div>
<div class="line"><a name="l00117"></a><span class="lineno"> 117</span>  }</div>
<div class="line"><a name="l00118"></a><span class="lineno"> 118</span> </div>
<div class="line"><a name="l00119"></a><span class="lineno"><a class="line" href="structOpenMS_1_1Internal_1_1MzIterator.html#aa9d1657a3991181d4328f63df98fae1a"> 119</a></span>  <span class="keyword">typename</span> FeaFiModuleType::IntensityType <a class="code" href="structOpenMS_1_1Internal_1_1MzIterator.html#aa9d1657a3991181d4328f63df98fae1a">operator*</a>()<span class="keyword"> const</span></div>
<div class="line"><a name="l00120"></a><span class="lineno"> 120</span> <span class="keyword"> </span>{</div>
<div class="line"><a name="l00121"></a><span class="lineno"> 121</span>  <span class="keywordflow">return</span> <a class="code" href="structOpenMS_1_1Internal_1_1MzIterator.html#a3a08b12523ea66ba7871e9bc5c6ce1b0">module_</a>->getPeakMz(FeatureFinderDefs::IndexSet::const_iterator::operator*());</div>
<div class="line"><a name="l00122"></a><span class="lineno"> 122</span>  }</div>
<div class="line"><a name="l00123"></a><span class="lineno"> 123</span> </div>
<div class="line"><a name="l00124"></a><span class="lineno"> 124</span> <span class="keyword">protected</span>:</div>
<div class="line"><a name="l00125"></a><span class="lineno"><a class="line" href="structOpenMS_1_1Internal_1_1MzIterator.html#a3a08b12523ea66ba7871e9bc5c6ce1b0"> 125</a></span>  <span class="keyword">const</span> FeaFiModuleType * <a class="code" href="structOpenMS_1_1Internal_1_1MzIterator.html#a3a08b12523ea66ba7871e9bc5c6ce1b0">module_</a>;</div>
<div class="line"><a name="l00126"></a><span class="lineno"> 126</span>  };</div>
<div class="line"><a name="l00127"></a><span class="lineno"> 127</span> </div>
<div class="line"><a name="l00128"></a><span class="lineno"> 128</span>  <span class="comment">//-------------------------------------------------------------------</span></div>
<div class="line"><a name="l00129"></a><span class="lineno"> 129</span> </div>
<div class="line"><a name="l00131"></a><span class="lineno"> 131</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> FeaFiModuleType></div>
<div class="line"><a name="l00132"></a><span class="lineno"><a class="line" href="structOpenMS_1_1Internal_1_1RtIterator.html"> 132</a></span>  <span class="keyword">struct </span><a class="code" href="structOpenMS_1_1Internal_1_1RtIterator.html">RtIterator</a> :</div>
<div class="line"><a name="l00133"></a><span class="lineno"> 133</span>  FeatureFinderDefs::IndexSet::const_iterator</div>
<div class="line"><a name="l00134"></a><span class="lineno"> 134</span>  {</div>
<div class="line"><a name="l00135"></a><span class="lineno"><a class="line" href="structOpenMS_1_1Internal_1_1RtIterator.html#a3cfc442fa2164d701b9837c73acc3e6c"> 135</a></span>  <a class="code" href="structOpenMS_1_1Internal_1_1RtIterator.html#a3cfc442fa2164d701b9837c73acc3e6c">RtIterator</a>(<span class="keyword">const</span> FeatureFinderDefs::IndexSet::const_iterator & iter, <span class="keyword">const</span> FeaFiModuleType * module) :</div>
<div class="line"><a name="l00136"></a><span class="lineno"> 136</span>  <a class="code" href="structOpenMS_1_1FeatureFinderDefs.html">FeatureFinderDefs</a>::IndexSet::const_iterator(iter),</div>
<div class="line"><a name="l00137"></a><span class="lineno"> 137</span>  <a class="code" href="structOpenMS_1_1Internal_1_1RtIterator.html#a3a08b12523ea66ba7871e9bc5c6ce1b0">module_</a>(module)</div>
<div class="line"><a name="l00138"></a><span class="lineno"> 138</span>  {</div>
<div class="line"><a name="l00139"></a><span class="lineno"> 139</span>  }</div>
<div class="line"><a name="l00140"></a><span class="lineno"> 140</span> </div>
<div class="line"><a name="l00141"></a><span class="lineno"><a class="line" href="structOpenMS_1_1Internal_1_1RtIterator.html#aa9d1657a3991181d4328f63df98fae1a"> 141</a></span>  <span class="keyword">typename</span> FeaFiModuleType::IntensityType <a class="code" href="structOpenMS_1_1Internal_1_1RtIterator.html#aa9d1657a3991181d4328f63df98fae1a">operator*</a>()<span class="keyword"> const</span></div>
<div class="line"><a name="l00142"></a><span class="lineno"> 142</span> <span class="keyword"> </span>{</div>
<div class="line"><a name="l00143"></a><span class="lineno"> 143</span>  <span class="keywordflow">return</span> <a class="code" href="structOpenMS_1_1Internal_1_1RtIterator.html#a3a08b12523ea66ba7871e9bc5c6ce1b0">module_</a>->getPeakRt(FeatureFinderDefs::IndexSet::const_iterator::operator*());</div>
<div class="line"><a name="l00144"></a><span class="lineno"> 144</span>  }</div>
<div class="line"><a name="l00145"></a><span class="lineno"> 145</span> </div>
<div class="line"><a name="l00146"></a><span class="lineno"> 146</span> <span class="keyword">protected</span>:</div>
<div class="line"><a name="l00147"></a><span class="lineno"><a class="line" href="structOpenMS_1_1Internal_1_1RtIterator.html#a3a08b12523ea66ba7871e9bc5c6ce1b0"> 147</a></span>  <span class="keyword">const</span> FeaFiModuleType * <a class="code" href="structOpenMS_1_1Internal_1_1RtIterator.html#a3a08b12523ea66ba7871e9bc5c6ce1b0">module_</a>;</div>
<div class="line"><a name="l00148"></a><span class="lineno"> 148</span>  };</div>
<div class="line"><a name="l00149"></a><span class="lineno"> 149</span> </div>
<div class="line"><a name="l00150"></a><span class="lineno"> 150</span>  <span class="comment">//-------------------------------------------------------------------</span></div>
<div class="line"><a name="l00151"></a><span class="lineno"> 151</span>  } <span class="comment">// namespace Internal</span></div>
<div class="line"><a name="l00152"></a><span class="lineno"> 152</span> </div>
<div class="line"><a name="l00156"></a><span class="lineno"> 156</span>  <span class="keyword">template</span> <<span class="keyword">class</span> PeakType, <span class="keyword">class</span> FeatureType></div>
<div class="line"><a name="l00157"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeaFiModule.html"> 157</a></span>  <span class="keyword">class </span><a class="code" href="classOpenMS_1_1FeaFiModule.html">FeaFiModule</a> :</div>
<div class="line"><a name="l00158"></a><span class="lineno"> 158</span>  <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></div>
<div class="line"><a name="l00159"></a><span class="lineno"> 159</span>  {</div>
<div class="line"><a name="l00160"></a><span class="lineno"> 160</span> <span class="keyword">public</span>:</div>
<div class="line"><a name="l00162"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeaFiModule.html#a21ea3968c35235b6b3cd78a2190280d9"> 162</a></span>  <span class="keyword">typedef</span> <a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap<FeatureType></a> <a class="code" href="classOpenMS_1_1FeaFiModule.html#a21ea3968c35235b6b3cd78a2190280d9">FeatureMapType</a>;</div>
<div class="line"><a name="l00164"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeaFiModule.html#adf6f376e844058d129ce8ba868276643"> 164</a></span>  <span class="keyword">typedef</span> <a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment<PeakType></a> <a class="code" href="classOpenMS_1_1FeaFiModule.html#adf6f376e844058d129ce8ba868276643">MapType</a>;</div>
<div class="line"><a name="l00166"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeaFiModule.html#ae4e0f0c176662a323a6a64d29ff986dd"> 166</a></span>  <span class="keyword">typedef</span> <span class="keyword">typename</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html">MapType::SpectrumType</a> <a class="code" href="classOpenMS_1_1FeaFiModule.html#ae4e0f0c176662a323a6a64d29ff986dd">SpectrumType</a>;</div>
<div class="line"><a name="l00168"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeaFiModule.html#a221361082f641c3fccc58e9bc66aeee1"> 168</a></span>  <span class="keyword">typedef</span> <span class="keyword">typename</span> <a class="code" href="classOpenMS_1_1Peak2D.html#a4a8c5b2adc05e9ff96a007385bfe9b47">PeakType::IntensityType</a> <a class="code" href="classOpenMS_1_1FeaFiModule.html#a221361082f641c3fccc58e9bc66aeee1">IntensityType</a>;</div>
<div class="line"><a name="l00170"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeaFiModule.html#a181486a43da338e31f089df7661f50bb"> 170</a></span>  <span class="keyword">typedef</span> <span class="keyword">typename</span> <a class="code" href="classdouble.html">PeakType::CoordinateType</a> <a class="code" href="classOpenMS_1_1FeaFiModule.html#a181486a43da338e31f089df7661f50bb">CoordinateType</a>;</div>
<div class="line"><a name="l00171"></a><span class="lineno"> 171</span> </div>
<div class="line"><a name="l00173"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeaFiModule.html#ad3fe3d27b98fcd12d996b358e30723fa"> 173</a></span>  <a class="code" href="classOpenMS_1_1FeaFiModule.html#ad3fe3d27b98fcd12d996b358e30723fa">FeaFiModule</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment<PeakType></a> * map, <a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap<FeatureType></a> * features, <a class="code" href="classOpenMS_1_1FeatureFinder.html">FeatureFinder</a> * ff) :</div>
<div class="line"><a name="l00174"></a><span class="lineno"> 174</span>  <a class="code" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a>(<span class="stringliteral">"FeaFiModule"</span>),</div>
<div class="line"><a name="l00175"></a><span class="lineno"> 175</span>  <a class="code" href="classOpenMS_1_1FeaFiModule.html#a365c5cf67d48519199fe00cb5688d628">map_</a>(0),</div>
<div class="line"><a name="l00176"></a><span class="lineno"> 176</span>  <a class="code" href="classOpenMS_1_1FeaFiModule.html#a5f09052343ef99616ad653897841ce3e">features_</a>(0),</div>
<div class="line"><a name="l00177"></a><span class="lineno"> 177</span>  <a class="code" href="classOpenMS_1_1FeaFiModule.html#adf68cb378c76b322b2cc4dbb2c145a3e">ff_</a>(0)</div>
<div class="line"><a name="l00178"></a><span class="lineno"> 178</span>  {</div>
<div class="line"><a name="l00179"></a><span class="lineno"> 179</span>  <a class="code" href="classOpenMS_1_1FeaFiModule.html#a365c5cf67d48519199fe00cb5688d628">map_</a> = map;</div>
<div class="line"><a name="l00180"></a><span class="lineno"> 180</span>  <a class="code" href="classOpenMS_1_1FeaFiModule.html#a5f09052343ef99616ad653897841ce3e">features_</a> = features;</div>
<div class="line"><a name="l00181"></a><span class="lineno"> 181</span>  <a class="code" href="classOpenMS_1_1FeaFiModule.html#adf68cb378c76b322b2cc4dbb2c145a3e">ff_</a> = ff;</div>
<div class="line"><a name="l00182"></a><span class="lineno"> 182</span>  }</div>
<div class="line"><a name="l00183"></a><span class="lineno"> 183</span> </div>
<div class="line"><a name="l00185"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeaFiModule.html#aa14dc0b3522c854b9005fc9dd5c754d3"> 185</a></span>  <span class="keyword">virtual</span> <a class="code" href="classOpenMS_1_1FeaFiModule.html#aa14dc0b3522c854b9005fc9dd5c754d3">~FeaFiModule</a>()</div>
<div class="line"><a name="l00186"></a><span class="lineno"> 186</span>  {</div>
<div class="line"><a name="l00187"></a><span class="lineno"> 187</span>  }</div>
<div class="line"><a name="l00188"></a><span class="lineno"> 188</span> </div>
<div class="line"><a name="l00190"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeaFiModule.html#a4698fa90bfbdd5729e0e25c62345ff0d"> 190</a></span>  <span class="keyword">inline</span> <a class="code" href="classOpenMS_1_1FeaFiModule.html#a221361082f641c3fccc58e9bc66aeee1">IntensityType</a> <a class="code" href="classOpenMS_1_1FeaFiModule.html#a4698fa90bfbdd5729e0e25c62345ff0d">getPeakIntensity</a>(<span class="keyword">const</span> <a class="code" href="structOpenMS_1_1FeatureFinderDefs.html#aaee0bfd850887fdc58115cead9e9b8b9">FeatureFinderDefs::IndexPair</a> & index)<span class="keyword"> const</span></div>
<div class="line"><a name="l00191"></a><span class="lineno"> 191</span> <span class="keyword"> </span>{</div>
<div class="line"><a name="l00192"></a><span class="lineno"> 192</span>  <span class="comment">//Corrupt index</span></div>
<div class="line"><a name="l00193"></a><span class="lineno"> 193</span>  <a class="code" href="group__Conditions.html#ga45a74ea28109e7e1ed992fbd2ee97778">OPENMS_PRECONDITION</a>(index.first < <a class="code" href="classOpenMS_1_1FeaFiModule.html#a365c5cf67d48519199fe00cb5688d628">map_</a>-><a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>(), <span class="stringliteral">"Scan index outside of map!"</span>);</div>
<div class="line"><a name="l00194"></a><span class="lineno"> 194</span>  <a class="code" href="group__Conditions.html#ga45a74ea28109e7e1ed992fbd2ee97778">OPENMS_PRECONDITION</a>(index.second < (*<a class="code" href="classOpenMS_1_1FeaFiModule.html#a365c5cf67d48519199fe00cb5688d628">map_</a>)[index.first].size(), <span class="stringliteral">"Peak index outside of scan!"</span>);</div>
<div class="line"><a name="l00195"></a><span class="lineno"> 195</span> </div>
<div class="line"><a name="l00196"></a><span class="lineno"> 196</span>  <span class="keywordflow">return</span> (*<a class="code" href="classOpenMS_1_1FeaFiModule.html#a365c5cf67d48519199fe00cb5688d628">map_</a>)[index.first][index.second].getIntensity();</div>
<div class="line"><a name="l00197"></a><span class="lineno"> 197</span>  }</div>
<div class="line"><a name="l00198"></a><span class="lineno"> 198</span> </div>
<div class="line"><a name="l00200"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeaFiModule.html#a606049d47faacd506705556d333849a2"> 200</a></span>  <span class="keyword">inline</span> <a class="code" href="classdouble.html">CoordinateType</a> <a class="code" href="classOpenMS_1_1FeaFiModule.html#a606049d47faacd506705556d333849a2">getPeakMz</a>(<span class="keyword">const</span> <a class="code" href="structOpenMS_1_1FeatureFinderDefs.html#aaee0bfd850887fdc58115cead9e9b8b9">FeatureFinderDefs::IndexPair</a> & index)<span class="keyword"> const</span></div>
<div class="line"><a name="l00201"></a><span class="lineno"> 201</span> <span class="keyword"> </span>{</div>
<div class="line"><a name="l00202"></a><span class="lineno"> 202</span>  <span class="comment">//Corrupt index</span></div>
<div class="line"><a name="l00203"></a><span class="lineno"> 203</span>  <a class="code" href="group__Conditions.html#ga45a74ea28109e7e1ed992fbd2ee97778">OPENMS_PRECONDITION</a>(index.first < <a class="code" href="classOpenMS_1_1FeaFiModule.html#a365c5cf67d48519199fe00cb5688d628">map_</a>-><a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>(), <span class="stringliteral">"Scan index outside of map!"</span>);</div>
<div class="line"><a name="l00204"></a><span class="lineno"> 204</span>  <a class="code" href="group__Conditions.html#ga45a74ea28109e7e1ed992fbd2ee97778">OPENMS_PRECONDITION</a>(index.second < (*<a class="code" href="classOpenMS_1_1FeaFiModule.html#a365c5cf67d48519199fe00cb5688d628">map_</a>)[index.first].size(), <span class="stringliteral">"Peak index outside of scan!"</span>);</div>
<div class="line"><a name="l00205"></a><span class="lineno"> 205</span> </div>
<div class="line"><a name="l00206"></a><span class="lineno"> 206</span>  <span class="keywordflow">return</span> (*<a class="code" href="classOpenMS_1_1FeaFiModule.html#a365c5cf67d48519199fe00cb5688d628">map_</a>)[index.first][index.second].getMZ();</div>
<div class="line"><a name="l00207"></a><span class="lineno"> 207</span>  }</div>
<div class="line"><a name="l00208"></a><span class="lineno"> 208</span> </div>
<div class="line"><a name="l00210"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeaFiModule.html#a8e5564d7b686645a7d7d6f5aed8cd494"> 210</a></span>  <span class="keyword">inline</span> <a class="code" href="classdouble.html">CoordinateType</a> <a class="code" href="classOpenMS_1_1FeaFiModule.html#a8e5564d7b686645a7d7d6f5aed8cd494">getPeakRt</a>(<span class="keyword">const</span> <a class="code" href="structOpenMS_1_1FeatureFinderDefs.html#aaee0bfd850887fdc58115cead9e9b8b9">FeatureFinderDefs::IndexPair</a> & index)<span class="keyword"> const</span></div>
<div class="line"><a name="l00211"></a><span class="lineno"> 211</span> <span class="keyword"> </span>{</div>
<div class="line"><a name="l00212"></a><span class="lineno"> 212</span>  <span class="comment">//Corrupt index</span></div>
<div class="line"><a name="l00213"></a><span class="lineno"> 213</span>  <a class="code" href="group__Conditions.html#ga45a74ea28109e7e1ed992fbd2ee97778">OPENMS_PRECONDITION</a>(index.first < <a class="code" href="classOpenMS_1_1FeaFiModule.html#a365c5cf67d48519199fe00cb5688d628">map_</a>-><a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>(), <span class="stringliteral">"Scan index outside of map!"</span>);</div>
<div class="line"><a name="l00214"></a><span class="lineno"> 214</span>  <a class="code" href="group__Conditions.html#ga45a74ea28109e7e1ed992fbd2ee97778">OPENMS_PRECONDITION</a>(index.second < (*<a class="code" href="classOpenMS_1_1FeaFiModule.html#a365c5cf67d48519199fe00cb5688d628">map_</a>)[index.first].size(), <span class="stringliteral">"Peak index outside of scan!"</span>);</div>
<div class="line"><a name="l00215"></a><span class="lineno"> 215</span> </div>
<div class="line"><a name="l00216"></a><span class="lineno"> 216</span>  <span class="keywordflow">return</span> (*<a class="code" href="classOpenMS_1_1FeaFiModule.html#a365c5cf67d48519199fe00cb5688d628">map_</a>)[index.first].getRT();</div>
<div class="line"><a name="l00217"></a><span class="lineno"> 217</span>  }</div>
<div class="line"><a name="l00218"></a><span class="lineno"> 218</span> </div>
<div class="line"><a name="l00225"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeaFiModule.html#a9f755c03fd9b7a485fec02224cc858d7"> 225</a></span>  <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1FeaFiModule.html#a9f755c03fd9b7a485fec02224cc858d7">getNextMz</a>(<a class="code" href="structOpenMS_1_1FeatureFinderDefs.html#aaee0bfd850887fdc58115cead9e9b8b9">FeatureFinderDefs::IndexPair</a> & index)<span class="keyword"> const</span></div>
<div class="line"><a name="l00226"></a><span class="lineno"> 226</span> <span class="keyword"> </span>{</div>
<div class="line"><a name="l00227"></a><span class="lineno"> 227</span>  <span class="comment">//Corrupt index</span></div>
<div class="line"><a name="l00228"></a><span class="lineno"> 228</span>  <a class="code" href="group__Conditions.html#ga45a74ea28109e7e1ed992fbd2ee97778">OPENMS_PRECONDITION</a>(index.first < <a class="code" href="classOpenMS_1_1FeaFiModule.html#a365c5cf67d48519199fe00cb5688d628">map_</a>-><a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>(), <span class="stringliteral">"Scan index outside of map!"</span>);</div>
<div class="line"><a name="l00229"></a><span class="lineno"> 229</span>  <a class="code" href="group__Conditions.html#ga45a74ea28109e7e1ed992fbd2ee97778">OPENMS_PRECONDITION</a>(index.second < (*<a class="code" href="classOpenMS_1_1FeaFiModule.html#a365c5cf67d48519199fe00cb5688d628">map_</a>)[index.first].size(), <span class="stringliteral">"Peak index outside of scan!"</span>);</div>
<div class="line"><a name="l00230"></a><span class="lineno"> 230</span> </div>
<div class="line"><a name="l00231"></a><span class="lineno"> 231</span>  <span class="comment">//At the last peak of this spectrum</span></div>
<div class="line"><a name="l00232"></a><span class="lineno"> 232</span>  <span class="keywordflow">if</span> (index.second + 1 >= (*<a class="code" href="classOpenMS_1_1FeaFiModule.html#a365c5cf67d48519199fe00cb5688d628">map_</a>)[index.first].size())</div>
<div class="line"><a name="l00233"></a><span class="lineno"> 233</span>  {</div>
<div class="line"><a name="l00234"></a><span class="lineno"> 234</span>  <span class="keywordflow">throw</span> <a class="code" href="classOpenMS_1_1FeatureFinderDefs_1_1NoSuccessor.html">FeatureFinderDefs::NoSuccessor</a>(__FILE__, __LINE__, <span class="stringliteral">"FeatureFinder::getNextMz"</span>, index);</div>
<div class="line"><a name="l00235"></a><span class="lineno"> 235</span>  }</div>
<div class="line"><a name="l00236"></a><span class="lineno"> 236</span> </div>
<div class="line"><a name="l00237"></a><span class="lineno"> 237</span>  ++index.second;</div>
<div class="line"><a name="l00238"></a><span class="lineno"> 238</span>  }</div>
<div class="line"><a name="l00239"></a><span class="lineno"> 239</span> </div>
<div class="line"><a name="l00246"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeaFiModule.html#a62c6d0208b4fc2bc51e55eea8ea1ce9d"> 246</a></span>  <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1FeaFiModule.html#a62c6d0208b4fc2bc51e55eea8ea1ce9d">getPrevMz</a>(<a class="code" href="structOpenMS_1_1FeatureFinderDefs.html#aaee0bfd850887fdc58115cead9e9b8b9">FeatureFinderDefs::IndexPair</a> & index)<span class="keyword"> const</span></div>
<div class="line"><a name="l00247"></a><span class="lineno"> 247</span> <span class="keyword"> </span>{</div>
<div class="line"><a name="l00248"></a><span class="lineno"> 248</span>  <span class="comment">//Corrupt index</span></div>
<div class="line"><a name="l00249"></a><span class="lineno"> 249</span>  <a class="code" href="group__Conditions.html#ga45a74ea28109e7e1ed992fbd2ee97778">OPENMS_PRECONDITION</a>(index.first < <a class="code" href="classOpenMS_1_1FeaFiModule.html#a365c5cf67d48519199fe00cb5688d628">map_</a>-><a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>(), <span class="stringliteral">"Scan index outside of map!"</span>);</div>
<div class="line"><a name="l00250"></a><span class="lineno"> 250</span>  <a class="code" href="group__Conditions.html#ga45a74ea28109e7e1ed992fbd2ee97778">OPENMS_PRECONDITION</a>(index.second < (*<a class="code" href="classOpenMS_1_1FeaFiModule.html#a365c5cf67d48519199fe00cb5688d628">map_</a>)[index.first].size(), <span class="stringliteral">"Peak index outside of scan!"</span>);</div>
<div class="line"><a name="l00251"></a><span class="lineno"> 251</span> </div>
<div class="line"><a name="l00252"></a><span class="lineno"> 252</span>  <span class="comment">//begin of scan</span></div>
<div class="line"><a name="l00253"></a><span class="lineno"> 253</span>  <span class="keywordflow">if</span> (index.second == 0)</div>
<div class="line"><a name="l00254"></a><span class="lineno"> 254</span>  {</div>
<div class="line"><a name="l00255"></a><span class="lineno"> 255</span>  <span class="keywordflow">throw</span> <a class="code" href="classOpenMS_1_1FeatureFinderDefs_1_1NoSuccessor.html">FeatureFinderDefs::NoSuccessor</a>(__FILE__, __LINE__, <span class="stringliteral">"FeatureFinder::getPrevMz"</span>, index);</div>
<div class="line"><a name="l00256"></a><span class="lineno"> 256</span>  }</div>
<div class="line"><a name="l00257"></a><span class="lineno"> 257</span> </div>
<div class="line"><a name="l00258"></a><span class="lineno"> 258</span>  --index.second;</div>
<div class="line"><a name="l00259"></a><span class="lineno"> 259</span>  }</div>
<div class="line"><a name="l00260"></a><span class="lineno"> 260</span> </div>
<div class="line"><a name="l00267"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeaFiModule.html#adf52c00b457571ad74d59a5d6fd12d1a"> 267</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1FeaFiModule.html#adf52c00b457571ad74d59a5d6fd12d1a">getNextRt</a>(<a class="code" href="structOpenMS_1_1FeatureFinderDefs.html#aaee0bfd850887fdc58115cead9e9b8b9">FeatureFinderDefs::IndexPair</a> & index)</div>
<div class="line"><a name="l00268"></a><span class="lineno"> 268</span>  {</div>
<div class="line"><a name="l00269"></a><span class="lineno"> 269</span>  <span class="comment">//Corrupt index</span></div>
<div class="line"><a name="l00270"></a><span class="lineno"> 270</span>  <a class="code" href="group__Conditions.html#ga45a74ea28109e7e1ed992fbd2ee97778">OPENMS_PRECONDITION</a>(index.first < <a class="code" href="classOpenMS_1_1FeaFiModule.html#a365c5cf67d48519199fe00cb5688d628">map_</a>-><a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>(), <span class="stringliteral">"Scan index outside of map!"</span>);</div>
<div class="line"><a name="l00271"></a><span class="lineno"> 271</span>  <a class="code" href="group__Conditions.html#ga45a74ea28109e7e1ed992fbd2ee97778">OPENMS_PRECONDITION</a>(index.second < (*<a class="code" href="classOpenMS_1_1FeaFiModule.html#a365c5cf67d48519199fe00cb5688d628">map_</a>)[index.first].size(), <span class="stringliteral">"Peak index outside of scan!"</span>);</div>
<div class="line"><a name="l00272"></a><span class="lineno"> 272</span> </div>
<div class="line"><a name="l00273"></a><span class="lineno"> 273</span>  <a class="code" href="classdouble.html">CoordinateType</a> mz_pos = (*map_)[index.first][index.second].getMZ(); <span class="comment">// mz value we want to find</span></div>
<div class="line"><a name="l00274"></a><span class="lineno"> 274</span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> index_first_tmp = index.first;</div>
<div class="line"><a name="l00275"></a><span class="lineno"> 275</span> </div>
<div class="line"><a name="l00276"></a><span class="lineno"> 276</span>  ++index.first;</div>
<div class="line"><a name="l00277"></a><span class="lineno"> 277</span>  <span class="keywordflow">while</span> (index.first < <a class="code" href="classOpenMS_1_1FeaFiModule.html#a365c5cf67d48519199fe00cb5688d628">map_</a>-><a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>() &&</div>
<div class="line"><a name="l00278"></a><span class="lineno"> 278</span>  (*map_)[index.first].empty())</div>
<div class="line"><a name="l00279"></a><span class="lineno"> 279</span>  {</div>
<div class="line"><a name="l00280"></a><span class="lineno"> 280</span>  ++index.first;</div>
<div class="line"><a name="l00281"></a><span class="lineno"> 281</span>  }</div>
<div class="line"><a name="l00282"></a><span class="lineno"> 282</span>  <span class="comment">//last scan</span></div>
<div class="line"><a name="l00283"></a><span class="lineno"> 283</span>  <span class="keywordflow">if</span> (index.first >= <a class="code" href="classOpenMS_1_1FeaFiModule.html#a365c5cf67d48519199fe00cb5688d628">map_</a>-><a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>())</div>
<div class="line"><a name="l00284"></a><span class="lineno"> 284</span>  {</div>
<div class="line"><a name="l00285"></a><span class="lineno"> 285</span>  <span class="keywordflow">throw</span> <a class="code" href="classOpenMS_1_1FeatureFinderDefs_1_1NoSuccessor.html">FeatureFinderDefs::NoSuccessor</a>(__FILE__, __LINE__, <span class="stringliteral">"FeatureFinder::getNextRt"</span>, index);</div>
<div class="line"><a name="l00286"></a><span class="lineno"> 286</span>  }</div>
<div class="line"><a name="l00287"></a><span class="lineno"> 287</span>  <span class="comment">// now we have a spectrum with scans in it ...</span></div>
<div class="line"><a name="l00288"></a><span class="lineno"> 288</span> </div>
<div class="line"><a name="l00289"></a><span class="lineno"> 289</span>  <span class="comment">// perform binary search to find the neighbour in mz dimension</span></div>
<div class="line"><a name="l00290"></a><span class="lineno"> 290</span>  <span class="keyword">typename</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html#a4895afe86c2aa0747ae0411c58c82114">SpectrumType::ConstIterator</a> it = lower_bound((*<a class="code" href="classOpenMS_1_1FeaFiModule.html#a365c5cf67d48519199fe00cb5688d628">map_</a>)[index.first].begin(), (*map_)[index.first].end(), (*map_)[index_first_tmp][index.second], <span class="keyword">typename</span> <a class="code" href="structOpenMS_1_1Peak2D_1_1PositionLess.html">PeakType::PositionLess</a>());</div>
<div class="line"><a name="l00291"></a><span class="lineno"> 291</span> </div>
<div class="line"><a name="l00292"></a><span class="lineno"> 292</span>  <span class="comment">// if the found peak is at the end of the spectrum, there is not much we can do...</span></div>
<div class="line"><a name="l00293"></a><span class="lineno"> 293</span>  <span class="keywordflow">if</span> (it == (*<a class="code" href="classOpenMS_1_1FeaFiModule.html#a365c5cf67d48519199fe00cb5688d628">map_</a>)[index.first].end())</div>
<div class="line"><a name="l00294"></a><span class="lineno"> 294</span>  {</div>
<div class="line"><a name="l00295"></a><span class="lineno"> 295</span>  index.second = (*map_)[index.first].size() - 1;</div>
<div class="line"><a name="l00296"></a><span class="lineno"> 296</span>  }</div>
<div class="line"><a name="l00297"></a><span class="lineno"> 297</span>  <span class="comment">// if the found peak is at the beginning of the spectrum, there is also not much we can do !</span></div>
<div class="line"><a name="l00298"></a><span class="lineno"> 298</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (it == (*<a class="code" href="classOpenMS_1_1FeaFiModule.html#a365c5cf67d48519199fe00cb5688d628">map_</a>)[index.first].begin())</div>
<div class="line"><a name="l00299"></a><span class="lineno"> 299</span>  {</div>
<div class="line"><a name="l00300"></a><span class="lineno"> 300</span>  index.second = 0;</div>
<div class="line"><a name="l00301"></a><span class="lineno"> 301</span>  }</div>
<div class="line"><a name="l00302"></a><span class="lineno"> 302</span>  <span class="comment">// see if the next smaller one fits better</span></div>
<div class="line"><a name="l00303"></a><span class="lineno"> 303</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00304"></a><span class="lineno"> 304</span>  {</div>
<div class="line"><a name="l00305"></a><span class="lineno"> 305</span>  <span class="comment">// peak to the right is closer (in m/z dimension)</span></div>
<div class="line"><a name="l00306"></a><span class="lineno"> 306</span>  <span class="keywordflow">if</span> (it->getMZ() - mz_pos < mz_pos - (it - 1)->getMZ())</div>
<div class="line"><a name="l00307"></a><span class="lineno"> 307</span>  {</div>
<div class="line"><a name="l00308"></a><span class="lineno"> 308</span>  index.second = it - (*map_)[index.first].begin();</div>
<div class="line"><a name="l00309"></a><span class="lineno"> 309</span>  }</div>
<div class="line"><a name="l00310"></a><span class="lineno"> 310</span>  <span class="keywordflow">else</span> <span class="comment">// left one is closer</span></div>
<div class="line"><a name="l00311"></a><span class="lineno"> 311</span>  {</div>
<div class="line"><a name="l00312"></a><span class="lineno"> 312</span>  index.second = --it - (*map_)[index.first].begin();</div>
<div class="line"><a name="l00313"></a><span class="lineno"> 313</span>  }</div>
<div class="line"><a name="l00314"></a><span class="lineno"> 314</span>  }</div>
<div class="line"><a name="l00315"></a><span class="lineno"> 315</span>  }</div>
<div class="line"><a name="l00316"></a><span class="lineno"> 316</span> </div>
<div class="line"><a name="l00323"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeaFiModule.html#ad4efb644d8a117edfaf7f0f5a9b34e0a"> 323</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1FeaFiModule.html#ad4efb644d8a117edfaf7f0f5a9b34e0a">getPrevRt</a>(<a class="code" href="structOpenMS_1_1FeatureFinderDefs.html#aaee0bfd850887fdc58115cead9e9b8b9">FeatureFinderDefs::IndexPair</a> & index)</div>
<div class="line"><a name="l00324"></a><span class="lineno"> 324</span>  {</div>
<div class="line"><a name="l00325"></a><span class="lineno"> 325</span>  <span class="comment">//Corrupt index</span></div>
<div class="line"><a name="l00326"></a><span class="lineno"> 326</span>  <a class="code" href="group__Conditions.html#ga45a74ea28109e7e1ed992fbd2ee97778">OPENMS_PRECONDITION</a>(index.first < <a class="code" href="classOpenMS_1_1FeaFiModule.html#a365c5cf67d48519199fe00cb5688d628">map_</a>-><a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>(), <span class="stringliteral">"Scan index outside of map!"</span>);</div>
<div class="line"><a name="l00327"></a><span class="lineno"> 327</span>  <a class="code" href="group__Conditions.html#ga45a74ea28109e7e1ed992fbd2ee97778">OPENMS_PRECONDITION</a>(index.second < (*<a class="code" href="classOpenMS_1_1FeaFiModule.html#a365c5cf67d48519199fe00cb5688d628">map_</a>)[index.first].size(), <span class="stringliteral">"Peak index outside of scan!"</span>);</div>
<div class="line"><a name="l00328"></a><span class="lineno"> 328</span> </div>
<div class="line"><a name="l00329"></a><span class="lineno"> 329</span>  <span class="comment">// TODO: this seems useless (at least for debug mode) given preconditions above... (and why not in getNextRt()??)</span></div>
<div class="line"><a name="l00330"></a><span class="lineno"> 330</span>  <span class="keywordflow">if</span> (index.first >= <a class="code" href="classOpenMS_1_1FeaFiModule.html#a365c5cf67d48519199fe00cb5688d628">map_</a>-><a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>())</div>
<div class="line"><a name="l00331"></a><span class="lineno"> 331</span>  {</div>
<div class="line"><a name="l00332"></a><span class="lineno"> 332</span>  std::cout << <span class="stringliteral">"Scan index outside of map!"</span> << std::endl;</div>
<div class="line"><a name="l00333"></a><span class="lineno"> 333</span>  std::cout << index.first << <span class="stringliteral">" "</span> << index.second << std::endl;</div>
<div class="line"><a name="l00334"></a><span class="lineno"> 334</span>  <span class="keywordflow">return</span>;</div>
<div class="line"><a name="l00335"></a><span class="lineno"> 335</span>  }</div>
<div class="line"><a name="l00336"></a><span class="lineno"> 336</span>  <span class="keywordflow">if</span> (index.second >= (*<a class="code" href="classOpenMS_1_1FeaFiModule.html#a365c5cf67d48519199fe00cb5688d628">map_</a>)[index.first].size())</div>
<div class="line"><a name="l00337"></a><span class="lineno"> 337</span>  {</div>
<div class="line"><a name="l00338"></a><span class="lineno"> 338</span>  std::cout << <span class="stringliteral">"Peak index outside of scan!"</span> << std::endl;</div>
<div class="line"><a name="l00339"></a><span class="lineno"> 339</span>  std::cout << index.first << <span class="stringliteral">" "</span> << index.second << std::endl;</div>
<div class="line"><a name="l00340"></a><span class="lineno"> 340</span>  <span class="keywordflow">return</span>;</div>
<div class="line"><a name="l00341"></a><span class="lineno"> 341</span>  }</div>
<div class="line"><a name="l00342"></a><span class="lineno"> 342</span> </div>
<div class="line"><a name="l00343"></a><span class="lineno"> 343</span>  <a class="code" href="classdouble.html">CoordinateType</a> mz_pos = (*map_)[index.first][index.second].getMZ();</div>
<div class="line"><a name="l00344"></a><span class="lineno"> 344</span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> index_first_tmp = index.first;</div>
<div class="line"><a name="l00345"></a><span class="lineno"> 345</span> </div>
<div class="line"><a name="l00346"></a><span class="lineno"> 346</span>  <span class="comment">// first scan</span></div>
<div class="line"><a name="l00347"></a><span class="lineno"> 347</span>  <span class="keywordflow">if</span> (index.first == 0)</div>
<div class="line"><a name="l00348"></a><span class="lineno"> 348</span>  {</div>
<div class="line"><a name="l00349"></a><span class="lineno"> 349</span>  <span class="keywordflow">throw</span> <a class="code" href="classOpenMS_1_1FeatureFinderDefs_1_1NoSuccessor.html">FeatureFinderDefs::NoSuccessor</a>(__FILE__, __LINE__, <span class="stringliteral">"FeatureFinder::getPrevRt"</span>, index);</div>
<div class="line"><a name="l00350"></a><span class="lineno"> 350</span>  }</div>
<div class="line"><a name="l00351"></a><span class="lineno"> 351</span> </div>
<div class="line"><a name="l00352"></a><span class="lineno"> 352</span>  --index.first;</div>
<div class="line"><a name="l00353"></a><span class="lineno"> 353</span>  <span class="keywordflow">while</span> ((index.first > 0) && ((*<a class="code" href="classOpenMS_1_1FeaFiModule.html#a365c5cf67d48519199fe00cb5688d628">map_</a>)[index.first].empty()))</div>
<div class="line"><a name="l00354"></a><span class="lineno"> 354</span>  {</div>
<div class="line"><a name="l00355"></a><span class="lineno"> 355</span>  --index.first;</div>
<div class="line"><a name="l00356"></a><span class="lineno"> 356</span>  }</div>
<div class="line"><a name="l00357"></a><span class="lineno"> 357</span>  <span class="comment">// we only found an empty scan</span></div>
<div class="line"><a name="l00358"></a><span class="lineno"> 358</span>  <span class="keywordflow">if</span> ((*<a class="code" href="classOpenMS_1_1FeaFiModule.html#a365c5cf67d48519199fe00cb5688d628">map_</a>)[index.first].empty()) <span class="keywordflow">throw</span> <a class="code" href="classOpenMS_1_1FeatureFinderDefs_1_1NoSuccessor.html">FeatureFinderDefs::NoSuccessor</a>(__FILE__, __LINE__, <span class="stringliteral">"FeatureFinder::getPrevRt"</span>, index);</div>
<div class="line"><a name="l00359"></a><span class="lineno"> 359</span> </div>
<div class="line"><a name="l00360"></a><span class="lineno"> 360</span>  <span class="comment">// perform binary search to find the neighbour in mz dimension</span></div>
<div class="line"><a name="l00361"></a><span class="lineno"> 361</span> </div>
<div class="line"><a name="l00362"></a><span class="lineno"> 362</span>  <span class="keyword">typename</span> <a class="code" href="classOpenMS_1_1MSExperiment.html#aee0a1a68d0fab63eefa6e14010b4a7f0">MapType::SpectrumType::ConstIterator</a> it = lower_bound((*<a class="code" href="classOpenMS_1_1FeaFiModule.html#a365c5cf67d48519199fe00cb5688d628">map_</a>)[index.first].begin(),</div>
<div class="line"><a name="l00363"></a><span class="lineno"> 363</span>  (*map_)[index.first].end(),</div>
<div class="line"><a name="l00364"></a><span class="lineno"> 364</span>  (*map_)[index_first_tmp][index.second],</div>
<div class="line"><a name="l00365"></a><span class="lineno"> 365</span>  <span class="keyword">typename</span> <a class="code" href="structOpenMS_1_1Peak2D_1_1PositionLess.html">PeakType::PositionLess</a>());</div>
<div class="line"><a name="l00366"></a><span class="lineno"> 366</span> </div>
<div class="line"><a name="l00367"></a><span class="lineno"> 367</span>  <span class="comment">// if the found peak is at the end of the spectrum, there is not much we can do.</span></div>
<div class="line"><a name="l00368"></a><span class="lineno"> 368</span>  <span class="keywordflow">if</span> (it == (*<a class="code" href="classOpenMS_1_1FeaFiModule.html#a365c5cf67d48519199fe00cb5688d628">map_</a>)[index.first].end())</div>
<div class="line"><a name="l00369"></a><span class="lineno"> 369</span>  {</div>
<div class="line"><a name="l00370"></a><span class="lineno"> 370</span>  index.second = (*map_)[index.first].size() - 1;</div>
<div class="line"><a name="l00371"></a><span class="lineno"> 371</span>  }</div>
<div class="line"><a name="l00372"></a><span class="lineno"> 372</span>  <span class="comment">// if the found peak is at the beginning of the spectrum, there is not much we can do.</span></div>
<div class="line"><a name="l00373"></a><span class="lineno"> 373</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (it == (*<a class="code" href="classOpenMS_1_1FeaFiModule.html#a365c5cf67d48519199fe00cb5688d628">map_</a>)[index.first].begin())</div>
<div class="line"><a name="l00374"></a><span class="lineno"> 374</span>  {</div>
<div class="line"><a name="l00375"></a><span class="lineno"> 375</span>  index.second = 0;</div>
<div class="line"><a name="l00376"></a><span class="lineno"> 376</span>  }</div>
<div class="line"><a name="l00377"></a><span class="lineno"> 377</span>  <span class="comment">// see if the next smaller one fits better</span></div>
<div class="line"><a name="l00378"></a><span class="lineno"> 378</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00379"></a><span class="lineno"> 379</span>  {</div>
<div class="line"><a name="l00380"></a><span class="lineno"> 380</span>  <span class="comment">// peak to the right is closer (in m/z dimension)</span></div>
<div class="line"><a name="l00381"></a><span class="lineno"> 381</span>  <span class="keywordflow">if</span> (it->getMZ() - mz_pos < mz_pos - (it - 1)->getMZ())</div>
<div class="line"><a name="l00382"></a><span class="lineno"> 382</span>  {</div>
<div class="line"><a name="l00383"></a><span class="lineno"> 383</span>  index.second = it - (*map_)[index.first].begin();</div>
<div class="line"><a name="l00384"></a><span class="lineno"> 384</span>  }</div>
<div class="line"><a name="l00385"></a><span class="lineno"> 385</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00386"></a><span class="lineno"> 386</span>  {</div>
<div class="line"><a name="l00387"></a><span class="lineno"> 387</span>  index.second = --it - (*map_)[index.first].begin();</div>
<div class="line"><a name="l00388"></a><span class="lineno"> 388</span>  }</div>
<div class="line"><a name="l00389"></a><span class="lineno"> 389</span>  }</div>
<div class="line"><a name="l00390"></a><span class="lineno"> 390</span>  }</div>
<div class="line"><a name="l00391"></a><span class="lineno"> 391</span> </div>
<div class="line"><a name="l00393"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeaFiModule.html#ac641d17ba54cde66c331d17bdee355e8"> 393</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1FeaFiModule.html#ac641d17ba54cde66c331d17bdee355e8">addConvexHull</a>(<span class="keyword">const</span> <a class="code" href="structOpenMS_1_1FeatureFinderDefs.html#af7439235b89a75354a2e87350e36834f">FeatureFinderDefs::IndexSet</a> & set, <a class="code" href="classOpenMS_1_1Feature.html">Feature</a> & feature)<span class="keyword"> const</span></div>
<div class="line"><a name="l00394"></a><span class="lineno"> 394</span> <span class="keyword"> </span>{</div>
<div class="line"><a name="l00395"></a><span class="lineno"> 395</span>  std::vector<DPosition<2> > points;</div>
<div class="line"><a name="l00396"></a><span class="lineno"> 396</span>  points.reserve(set.size());</div>
<div class="line"><a name="l00397"></a><span class="lineno"> 397</span>  <a class="code" href="classOpenMS_1_1DPosition.html">DPosition<2></a> tmp;</div>
<div class="line"><a name="l00398"></a><span class="lineno"> 398</span>  <span class="keywordflow">for</span> (FeatureFinderDefs::IndexSet::const_iterator it = set.begin(); it != set.end(); ++it)</div>
<div class="line"><a name="l00399"></a><span class="lineno"> 399</span>  {</div>
<div class="line"><a name="l00400"></a><span class="lineno"> 400</span>  tmp[<a class="code" href="classOpenMS_1_1Peak2D.html#ac2d92631c8f762c7e9afe43f11e1f018a35008b046ec2687e53152082281d0867">Peak2D::MZ</a>] = (*map_)[it->first][it->second].getMZ();</div>
<div class="line"><a name="l00401"></a><span class="lineno"> 401</span>  tmp[<a class="code" href="classOpenMS_1_1Peak2D.html#ac2d92631c8f762c7e9afe43f11e1f018af388fcb6d444ef59841ef549ca6ee0da">Peak2D::RT</a>] = (*map_)[it->first].getRT();</div>
<div class="line"><a name="l00402"></a><span class="lineno"> 402</span>  points.push_back(tmp);</div>
<div class="line"><a name="l00403"></a><span class="lineno"> 403</span>  }</div>
<div class="line"><a name="l00404"></a><span class="lineno"> 404</span>  feature.<a class="code" href="classOpenMS_1_1Feature.html#ad99bb8ba2103d6c52ee10ae6369b46e7">getConvexHulls</a>().resize(feature.<a class="code" href="classOpenMS_1_1Feature.html#ad99bb8ba2103d6c52ee10ae6369b46e7">getConvexHulls</a>().size() + 1);</div>
<div class="line"><a name="l00405"></a><span class="lineno"> 405</span>  <span class="comment">// computes convex hull</span></div>
<div class="line"><a name="l00406"></a><span class="lineno"> 406</span>  feature.<a class="code" href="classOpenMS_1_1Feature.html#ad99bb8ba2103d6c52ee10ae6369b46e7">getConvexHulls</a>().back().addPoints(points);</div>
<div class="line"><a name="l00407"></a><span class="lineno"> 407</span>  }</div>
<div class="line"><a name="l00408"></a><span class="lineno"> 408</span> </div>
<div class="line"><a name="l00409"></a><span class="lineno"> 409</span> <span class="keyword">protected</span>:</div>
<div class="line"><a name="l00411"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeaFiModule.html#a365c5cf67d48519199fe00cb5688d628"> 411</a></span>  <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSExperiment.html">MapType</a> * <a class="code" href="classOpenMS_1_1FeaFiModule.html#a365c5cf67d48519199fe00cb5688d628">map_</a>;</div>
<div class="line"><a name="l00413"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeaFiModule.html#a5f09052343ef99616ad653897841ce3e"> 413</a></span>  <a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMapType</a> * <a class="code" href="classOpenMS_1_1FeaFiModule.html#a5f09052343ef99616ad653897841ce3e">features_</a>;</div>
<div class="line"><a name="l00415"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeaFiModule.html#adf68cb378c76b322b2cc4dbb2c145a3e"> 415</a></span>  <a class="code" href="classOpenMS_1_1FeatureFinder.html">FeatureFinder</a> * <a class="code" href="classOpenMS_1_1FeaFiModule.html#adf68cb378c76b322b2cc4dbb2c145a3e">ff_</a>;</div>
<div class="line"><a name="l00416"></a><span class="lineno"> 416</span> </div>
<div class="line"><a name="l00417"></a><span class="lineno"> 417</span> <span class="keyword">private</span>:</div>
<div class="line"><a name="l00419"></a><span class="lineno"> 419</span>  <a class="code" href="classOpenMS_1_1FeaFiModule.html#aa769c6ab217b68ae46061d722ff7f5d1">FeaFiModule</a>();</div>
<div class="line"><a name="l00421"></a><span class="lineno"> 421</span>  <a class="code" href="classOpenMS_1_1FeaFiModule.html">FeaFiModule</a> & <a class="code" href="classOpenMS_1_1FeaFiModule.html#a58dbffc498123ad5d8d371843a9e6d5b">operator=</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1FeaFiModule.html">FeaFiModule</a> &);</div>
<div class="line"><a name="l00423"></a><span class="lineno"> 423</span>  <a class="code" href="classOpenMS_1_1FeaFiModule.html#aa769c6ab217b68ae46061d722ff7f5d1">FeaFiModule</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1FeaFiModule.html">FeaFiModule</a> &);</div>
<div class="line"><a name="l00424"></a><span class="lineno"> 424</span> </div>
<div class="line"><a name="l00425"></a><span class="lineno"> 425</span>  }; <span class="comment">// class FeaFiModule</span></div>
<div class="line"><a name="l00426"></a><span class="lineno"> 426</span> </div>
<div class="line"><a name="l00427"></a><span class="lineno"> 427</span> } <span class="comment">// namespace OpenMS</span></div>
<div class="line"><a name="l00428"></a><span class="lineno"> 428</span> </div>
<div class="line"><a name="l00429"></a><span class="lineno"> 429</span> <span class="preprocessor">#endif // OPENMS_TRANSFORMATIONS_FEATUREFINDER_FEAFIMODULE_H</span></div>
<div class="ttc" id="classOpenMS_1_1FeaFiModule_html"><div class="ttname"><a href="classOpenMS_1_1FeaFiModule.html">OpenMS::FeaFiModule</a></div><div class="ttdoc">Implements a module of the FeatureFinder algorithm. </div><div class="ttdef"><b>Definition:</b> FeaFiModule.h:157</div></div>
<div class="ttc" id="classOpenMS_1_1Peak2D_html_a4a8c5b2adc05e9ff96a007385bfe9b47"><div class="ttname"><a href="classOpenMS_1_1Peak2D.html#a4a8c5b2adc05e9ff96a007385bfe9b47">OpenMS::Peak2D::IntensityType</a></div><div class="ttdeci">Real IntensityType</div><div class="ttdoc">Intensity type. </div><div class="ttdef"><b>Definition:</b> Peak2D.h:63</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_1FeaFiModule_html_a9f755c03fd9b7a485fec02224cc858d7"><div class="ttname"><a href="classOpenMS_1_1FeaFiModule.html#a9f755c03fd9b7a485fec02224cc858d7">OpenMS::FeaFiModule::getNextMz</a></div><div class="ttdeci">void getNextMz(FeatureFinderDefs::IndexPair &index) const </div><div class="ttdoc">fills index with the index of next peak in m/z dimension </div><div class="ttdef"><b>Definition:</b> FeaFiModule.h:225</div></div>
<div class="ttc" id="classOpenMS_1_1FeaFiModule_html_a8e5564d7b686645a7d7d6f5aed8cd494"><div class="ttname"><a href="classOpenMS_1_1FeaFiModule.html#a8e5564d7b686645a7d7d6f5aed8cd494">OpenMS::FeaFiModule::getPeakRt</a></div><div class="ttdeci">CoordinateType getPeakRt(const FeatureFinderDefs::IndexPair &index) const </div><div class="ttdoc">Returns the retention time of a peak. </div><div class="ttdef"><b>Definition:</b> FeaFiModule.h:210</div></div>
<div class="ttc" id="structOpenMS_1_1Internal_1_1IntensityIterator_html_aa3fbcf8848df3dc4e06c441ef10b4de4"><div class="ttname"><a href="structOpenMS_1_1Internal_1_1IntensityIterator.html#aa3fbcf8848df3dc4e06c441ef10b4de4">OpenMS::Internal::IntensityIterator::IntensityIterator</a></div><div class="ttdeci">IntensityIterator(const FeatureFinderDefs::IndexSet::const_iterator &iter, const FeaFiModuleType *module)</div><div class="ttdef"><b>Definition:</b> FeaFiModule.h:91</div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html_a9d78a687cf2a391198bb3cbc08bc06cb"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">OpenMS::MSExperiment::size</a></div><div class="ttdeci">Size size() const </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:117</div></div>
<div class="ttc" id="classOpenMS_1_1FeaFiModule_html_a4698fa90bfbdd5729e0e25c62345ff0d"><div class="ttname"><a href="classOpenMS_1_1FeaFiModule.html#a4698fa90bfbdd5729e0e25c62345ff0d">OpenMS::FeaFiModule::getPeakIntensity</a></div><div class="ttdeci">IntensityType getPeakIntensity(const FeatureFinderDefs::IndexPair &index) const </div><div class="ttdoc">Returns the intensity of a peak. </div><div class="ttdef"><b>Definition:</b> FeaFiModule.h:190</div></div>
<div class="ttc" id="structOpenMS_1_1Internal_1_1IntensityLess_html_a6a3e75b9d7ab0a2dca8122e197b7fe5e"><div class="ttname"><a href="structOpenMS_1_1Internal_1_1IntensityLess.html#a6a3e75b9d7ab0a2dca8122e197b7fe5e">OpenMS::Internal::IntensityLess::IntensityLess</a></div><div class="ttdeci">IntensityLess(const IntensityLess &rhs)</div><div class="ttdoc">Copy ctor. </div><div class="ttdef"><b>Definition:</b> FeaFiModule.h:66</div></div>
<div class="ttc" id="classOpenMS_1_1FeaFiModule_html_a5f09052343ef99616ad653897841ce3e"><div class="ttname"><a href="classOpenMS_1_1FeaFiModule.html#a5f09052343ef99616ad653897841ce3e">OpenMS::FeaFiModule::features_</a></div><div class="ttdeci">FeatureMapType * features_</div><div class="ttdoc">Output data pointer. </div><div class="ttdef"><b>Definition:</b> FeaFiModule.h:413</div></div>
<div class="ttc" id="classOpenMS_1_1Peak2D_html_ac2d92631c8f762c7e9afe43f11e1f018af388fcb6d444ef59841ef549ca6ee0da"><div class="ttname"><a href="classOpenMS_1_1Peak2D.html#ac2d92631c8f762c7e9afe43f11e1f018af388fcb6d444ef59841ef549ca6ee0da">OpenMS::Peak2D::RT</a></div><div class="ttdoc">Retention time dimension id (0 if used as a const int) </div><div class="ttdef"><b>Definition:</b> Peak2D.h:76</div></div>
<div class="ttc" id="classOpenMS_1_1FeaFiModule_html_adf52c00b457571ad74d59a5d6fd12d1a"><div class="ttname"><a href="classOpenMS_1_1FeaFiModule.html#adf52c00b457571ad74d59a5d6fd12d1a">OpenMS::FeaFiModule::getNextRt</a></div><div class="ttdeci">void getNextRt(FeatureFinderDefs::IndexPair &index)</div><div class="ttdoc">fills index with the index of the nearest peak in the next scan </div><div class="ttdef"><b>Definition:</b> FeaFiModule.h:267</div></div>
<div class="ttc" id="classOpenMS_1_1FeaFiModule_html_a221361082f641c3fccc58e9bc66aeee1"><div class="ttname"><a href="classOpenMS_1_1FeaFiModule.html#a221361082f641c3fccc58e9bc66aeee1">OpenMS::FeaFiModule::IntensityType</a></div><div class="ttdeci">PeakType::IntensityType IntensityType</div><div class="ttdoc">Input intensity type. </div><div class="ttdef"><b>Definition:</b> FeaFiModule.h:168</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureMap_html"><div class="ttname"><a href="classOpenMS_1_1FeatureMap.html">OpenMS::FeatureMap</a></div><div class="ttdoc">A container for features. </div><div class="ttdef"><b>Definition:</b> FeatureMap.h:111</div></div>
<div class="ttc" id="group__Conditions_html_ga45a74ea28109e7e1ed992fbd2ee97778"><div class="ttname"><a href="group__Conditions.html#ga45a74ea28109e7e1ed992fbd2ee97778">OPENMS_PRECONDITION</a></div><div class="ttdeci">#define OPENMS_PRECONDITION(condition, message)</div><div class="ttdoc">Precondition macro. </div><div class="ttdef"><b>Definition:</b> Macros.h:107</div></div>
<div class="ttc" id="classOpenMS_1_1MSSpectrum_html_a4895afe86c2aa0747ae0411c58c82114"><div class="ttname"><a href="classOpenMS_1_1MSSpectrum.html#a4895afe86c2aa0747ae0411c58c82114">OpenMS::MSSpectrum< PeakType >::ConstIterator</a></div><div class="ttdeci">ContainerType::const_iterator ConstIterator</div><div class="ttdoc">Non-mutable iterator. </div><div class="ttdef"><b>Definition:</b> MSSpectrum.h:125</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_1Internal_1_1IntensityLess_html_a35b8d10c84a677edb9fbd6de39f21c7b"><div class="ttname"><a href="structOpenMS_1_1Internal_1_1IntensityLess.html#a35b8d10c84a677edb9fbd6de39f21c7b">OpenMS::Internal::IntensityLess::IntensityLess</a></div><div class="ttdeci">IntensityLess()</div><div class="ttdoc">Default ctor undefined since we cannot compare without a FeaFiModule. </div></div>
<div class="ttc" id="classOpenMS_1_1Peak2D_html_ac2d92631c8f762c7e9afe43f11e1f018a35008b046ec2687e53152082281d0867"><div class="ttname"><a href="classOpenMS_1_1Peak2D.html#ac2d92631c8f762c7e9afe43f11e1f018a35008b046ec2687e53152082281d0867">OpenMS::Peak2D::MZ</a></div><div class="ttdoc">Mass-to-charge dimension id (1 if used as a const int) </div><div class="ttdef"><b>Definition:</b> Peak2D.h:77</div></div>
<div class="ttc" id="structOpenMS_1_1Internal_1_1RtIterator_html_aa9d1657a3991181d4328f63df98fae1a"><div class="ttname"><a href="structOpenMS_1_1Internal_1_1RtIterator.html#aa9d1657a3991181d4328f63df98fae1a">OpenMS::Internal::RtIterator::operator*</a></div><div class="ttdeci">FeaFiModuleType::IntensityType operator*() const </div><div class="ttdef"><b>Definition:</b> FeaFiModule.h:141</div></div>
<div class="ttc" id="classOpenMS_1_1FeaFiModule_html_a62c6d0208b4fc2bc51e55eea8ea1ce9d"><div class="ttname"><a href="classOpenMS_1_1FeaFiModule.html#a62c6d0208b4fc2bc51e55eea8ea1ce9d">OpenMS::FeaFiModule::getPrevMz</a></div><div class="ttdeci">void getPrevMz(FeatureFinderDefs::IndexPair &index) const </div><div class="ttdoc">fills index with the index of previous peak in m/z dimension </div><div class="ttdef"><b>Definition:</b> FeaFiModule.h:246</div></div>
<div class="ttc" id="DefaultParamHandler_8h_html"><div class="ttname"><a href="DefaultParamHandler_8h.html">DefaultParamHandler.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1FeaFiModule_html_adf68cb378c76b322b2cc4dbb2c145a3e"><div class="ttname"><a href="classOpenMS_1_1FeaFiModule.html#adf68cb378c76b322b2cc4dbb2c145a3e">OpenMS::FeaFiModule::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 and report progress...</div><div class="ttdef"><b>Definition:</b> FeaFiModule.h:415</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_1FeaFiModule_html_a365c5cf67d48519199fe00cb5688d628"><div class="ttname"><a href="classOpenMS_1_1FeaFiModule.html#a365c5cf67d48519199fe00cb5688d628">OpenMS::FeaFiModule::map_</a></div><div class="ttdeci">const MapType * map_</div><div class="ttdoc">Input data pointer. </div><div class="ttdef"><b>Definition:</b> FeaFiModule.h:411</div></div>
<div class="ttc" id="structOpenMS_1_1Peak2D_1_1PositionLess_html"><div class="ttname"><a href="structOpenMS_1_1Peak2D_1_1PositionLess.html">OpenMS::Peak2D::PositionLess</a></div><div class="ttdoc">Comparator by position. Lexicographical comparison (first RT then m/z) is done. </div><div class="ttdef"><b>Definition:</b> Peak2D.h:324</div></div>
<div class="ttc" id="classOpenMS_1_1FeaFiModule_html_a58dbffc498123ad5d8d371843a9e6d5b"><div class="ttname"><a href="classOpenMS_1_1FeaFiModule.html#a58dbffc498123ad5d8d371843a9e6d5b">OpenMS::FeaFiModule::operator=</a></div><div class="ttdeci">FeaFiModule & operator=(const FeaFiModule &)</div><div class="ttdoc">Not implemented. </div></div>
<div class="ttc" id="structOpenMS_1_1Internal_1_1RtIterator_html_a3cfc442fa2164d701b9837c73acc3e6c"><div class="ttname"><a href="structOpenMS_1_1Internal_1_1RtIterator.html#a3cfc442fa2164d701b9837c73acc3e6c">OpenMS::Internal::RtIterator::RtIterator</a></div><div class="ttdeci">RtIterator(const FeatureFinderDefs::IndexSet::const_iterator &iter, const FeaFiModuleType *module)</div><div class="ttdef"><b>Definition:</b> FeaFiModule.h:135</div></div>
<div class="ttc" id="structOpenMS_1_1Internal_1_1MzIterator_html_aa9d1657a3991181d4328f63df98fae1a"><div class="ttname"><a href="structOpenMS_1_1Internal_1_1MzIterator.html#aa9d1657a3991181d4328f63df98fae1a">OpenMS::Internal::MzIterator::operator*</a></div><div class="ttdeci">FeaFiModuleType::IntensityType operator*() const </div><div class="ttdef"><b>Definition:</b> FeaFiModule.h:119</div></div>
<div class="ttc" id="MSExperiment_8h_html"><div class="ttname"><a href="MSExperiment_8h.html">MSExperiment.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1MSSpectrum_html"><div class="ttname"><a href="classOpenMS_1_1MSSpectrum.html">OpenMS::MSSpectrum< PeakType ></a></div></div>
<div class="ttc" id="classOpenMS_1_1FeaFiModule_html_a606049d47faacd506705556d333849a2"><div class="ttname"><a href="classOpenMS_1_1FeaFiModule.html#a606049d47faacd506705556d333849a2">OpenMS::FeaFiModule::getPeakMz</a></div><div class="ttdeci">CoordinateType getPeakMz(const FeatureFinderDefs::IndexPair &index) const </div><div class="ttdoc">Returns the m/z of a peak. </div><div class="ttdef"><b>Definition:</b> FeaFiModule.h:200</div></div>
<div class="ttc" id="classOpenMS_1_1FeaFiModule_html_ad4efb644d8a117edfaf7f0f5a9b34e0a"><div class="ttname"><a href="classOpenMS_1_1FeaFiModule.html#ad4efb644d8a117edfaf7f0f5a9b34e0a">OpenMS::FeaFiModule::getPrevRt</a></div><div class="ttdeci">void getPrevRt(FeatureFinderDefs::IndexPair &index)</div><div class="ttdoc">fills index with the index of the nearest peak in the previous scan </div><div class="ttdef"><b>Definition:</b> FeaFiModule.h:323</div></div>
<div class="ttc" id="classOpenMS_1_1DPosition_html"><div class="ttname"><a href="classOpenMS_1_1DPosition.html">OpenMS::DPosition< 2 ></a></div></div>
<div class="ttc" id="structOpenMS_1_1Internal_1_1IntensityLess_html_a414b3def0d80594ea23bda8b4cd88b30"><div class="ttname"><a href="structOpenMS_1_1Internal_1_1IntensityLess.html#a414b3def0d80594ea23bda8b4cd88b30">OpenMS::Internal::IntensityLess::module_</a></div><div class="ttdeci">const FeaFiModuleType & module_</div><div class="ttdoc">Reference to the FeaFiModule. </div><div class="ttdef"><b>Definition:</b> FeaFiModule.h:79</div></div>
<div class="ttc" id="classOpenMS_1_1Feature_html_ad99bb8ba2103d6c52ee10ae6369b46e7"><div class="ttname"><a href="classOpenMS_1_1Feature.html#ad99bb8ba2103d6c52ee10ae6369b46e7">OpenMS::Feature::getConvexHulls</a></div><div class="ttdeci">const std::vector< ConvexHull2D > & getConvexHulls() const </div><div class="ttdoc">Non-mutable access to the convex hulls. </div></div>
<div class="ttc" id="structOpenMS_1_1FeatureFinderDefs_html_af7439235b89a75354a2e87350e36834f"><div class="ttname"><a href="structOpenMS_1_1FeatureFinderDefs.html#af7439235b89a75354a2e87350e36834f">OpenMS::FeatureFinderDefs::IndexSet</a></div><div class="ttdeci">IsotopeCluster::IndexSet IndexSet</div><div class="ttdoc">A set of peak indices. </div><div class="ttdef"><b>Definition:</b> FeatureFinderDefs.h:60</div></div>
<div class="ttc" id="classOpenMS_1_1FeaFiModule_html_ac641d17ba54cde66c331d17bdee355e8"><div class="ttname"><a href="classOpenMS_1_1FeaFiModule.html#ac641d17ba54cde66c331d17bdee355e8">OpenMS::FeaFiModule::addConvexHull</a></div><div class="ttdeci">void addConvexHull(const FeatureFinderDefs::IndexSet &set, Feature &feature) const </div><div class="ttdoc">Calculates the convex hull of a index set and adds it to the feature. </div><div class="ttdef"><b>Definition:</b> FeaFiModule.h:393</div></div>
<div class="ttc" id="structOpenMS_1_1Internal_1_1MzIterator_html_a3a08b12523ea66ba7871e9bc5c6ce1b0"><div class="ttname"><a href="structOpenMS_1_1Internal_1_1MzIterator.html#a3a08b12523ea66ba7871e9bc5c6ce1b0">OpenMS::Internal::MzIterator::module_</a></div><div class="ttdeci">const FeaFiModuleType * module_</div><div class="ttdef"><b>Definition:</b> FeaFiModule.h:125</div></div>
<div class="ttc" id="structOpenMS_1_1Internal_1_1RtIterator_html"><div class="ttname"><a href="structOpenMS_1_1Internal_1_1RtIterator.html">OpenMS::Internal::RtIterator</a></div><div class="ttdoc">Retention time iterator for a FeatureFinderDefs::IndexSet. </div><div class="ttdef"><b>Definition:</b> FeaFiModule.h:132</div></div>
<div class="ttc" id="structOpenMS_1_1Internal_1_1IntensityLess_html"><div class="ttname"><a href="structOpenMS_1_1Internal_1_1IntensityLess.html">OpenMS::Internal::IntensityLess</a></div><div class="ttdoc">Comparator that allows to compare the indices of two peaks by their intensity. </div><div class="ttdef"><b>Definition:</b> FeaFiModule.h:56</div></div>
<div class="ttc" id="structOpenMS_1_1Internal_1_1IntensityIterator_html_aa9d1657a3991181d4328f63df98fae1a"><div class="ttname"><a href="structOpenMS_1_1Internal_1_1IntensityIterator.html#aa9d1657a3991181d4328f63df98fae1a">OpenMS::Internal::IntensityIterator::operator*</a></div><div class="ttdeci">FeaFiModuleType::IntensityType operator*() const </div><div class="ttdef"><b>Definition:</b> FeaFiModule.h:97</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="structOpenMS_1_1Internal_1_1MzIterator_html_a5fa88c983f41e3ae1a39a41771f2daa2"><div class="ttname"><a href="structOpenMS_1_1Internal_1_1MzIterator.html#a5fa88c983f41e3ae1a39a41771f2daa2">OpenMS::Internal::MzIterator::MzIterator</a></div><div class="ttdeci">MzIterator(const FeatureFinderDefs::IndexSet::const_iterator &iter, const FeaFiModuleType *module)</div><div class="ttdef"><b>Definition:</b> FeaFiModule.h:113</div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html">OpenMS::MSExperiment</a></div><div class="ttdoc">Representation of a mass spectrometry experiment. </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:68</div></div>
<div class="ttc" id="FeatureFinderDefs_8h_html"><div class="ttname"><a href="FeatureFinderDefs_8h.html">FeatureFinderDefs.h</a></div></div>
<div class="ttc" id="structOpenMS_1_1Internal_1_1MzIterator_html"><div class="ttname"><a href="structOpenMS_1_1Internal_1_1MzIterator.html">OpenMS::Internal::MzIterator</a></div><div class="ttdoc">m/z iterator for a FeatureFinderDefs::IndexSet </div><div class="ttdef"><b>Definition:</b> FeaFiModule.h:110</div></div>
<div class="ttc" id="classOpenMS_1_1FeaFiModule_html_a181486a43da338e31f089df7661f50bb"><div class="ttname"><a href="classOpenMS_1_1FeaFiModule.html#a181486a43da338e31f089df7661f50bb">OpenMS::FeaFiModule::CoordinateType</a></div><div class="ttdeci">PeakType::CoordinateType CoordinateType</div><div class="ttdoc">Input coordinate type. </div><div class="ttdef"><b>Definition:</b> FeaFiModule.h:170</div></div>
<div class="ttc" id="structOpenMS_1_1Internal_1_1IntensityIterator_html"><div class="ttname"><a href="structOpenMS_1_1Internal_1_1IntensityIterator.html">OpenMS::Internal::IntensityIterator</a></div><div class="ttdoc">Intensity iterator for a FeatureFinderDefs::IndexSet. </div><div class="ttdef"><b>Definition:</b> FeaFiModule.h:88</div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html_aee0a1a68d0fab63eefa6e14010b4a7f0"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html#aee0a1a68d0fab63eefa6e14010b4a7f0">OpenMS::MSExperiment::ConstIterator</a></div><div class="ttdeci">std::vector< SpectrumType >::const_iterator ConstIterator</div><div class="ttdoc">Non-mutable iterator. </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:103</div></div>
<div class="ttc" id="classOpenMS_1_1FeaFiModule_html_aa769c6ab217b68ae46061d722ff7f5d1"><div class="ttname"><a href="classOpenMS_1_1FeaFiModule.html#aa769c6ab217b68ae46061d722ff7f5d1">OpenMS::FeaFiModule::FeaFiModule</a></div><div class="ttdeci">FeaFiModule()</div><div class="ttdoc">Not implemented. </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="structOpenMS_1_1Internal_1_1IntensityLess_html_a30c8699daaee3f695c0f7736e50b4829"><div class="ttname"><a href="structOpenMS_1_1Internal_1_1IntensityLess.html#a30c8699daaee3f695c0f7736e50b4829">OpenMS::Internal::IntensityLess::IntensityLess</a></div><div class="ttdeci">IntensityLess(const FeaFiModuleType &module)</div><div class="ttdoc">Constructor that takes a FeaFiModule reference. </div><div class="ttdef"><b>Definition:</b> FeaFiModule.h:60</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinder_html"><div class="ttname"><a href="classOpenMS_1_1FeatureFinder.html">OpenMS::FeatureFinder</a></div><div class="ttdoc">The main feature finder class. </div><div class="ttdef"><b>Definition:</b> FeatureFinder.h:57</div></div>
<div class="ttc" id="classOpenMS_1_1FeaFiModule_html_aa14dc0b3522c854b9005fc9dd5c754d3"><div class="ttname"><a href="classOpenMS_1_1FeaFiModule.html#aa14dc0b3522c854b9005fc9dd5c754d3">OpenMS::FeaFiModule::~FeaFiModule</a></div><div class="ttdeci">virtual ~FeaFiModule()</div><div class="ttdoc">destructor </div><div class="ttdef"><b>Definition:</b> FeaFiModule.h:185</div></div>
<div class="ttc" id="classOpenMS_1_1DefaultParamHandler_html"><div class="ttname"><a href="classOpenMS_1_1DefaultParamHandler.html">OpenMS::DefaultParamHandler</a></div><div class="ttdoc">A base class for all classes handling default parameters. </div><div class="ttdef"><b>Definition:</b> DefaultParamHandler.h:90</div></div>
<div class="ttc" id="classOpenMS_1_1FeaFiModule_html_adf6f376e844058d129ce8ba868276643"><div class="ttname"><a href="classOpenMS_1_1FeaFiModule.html#adf6f376e844058d129ce8ba868276643">OpenMS::FeaFiModule::MapType</a></div><div class="ttdeci">MSExperiment< PeakType > MapType</div><div class="ttdoc">Input map type. </div><div class="ttdef"><b>Definition:</b> FeaFiModule.h:164</div></div>
<div class="ttc" id="classOpenMS_1_1FeaFiModule_html_ae4e0f0c176662a323a6a64d29ff986dd"><div class="ttname"><a href="classOpenMS_1_1FeaFiModule.html#ae4e0f0c176662a323a6a64d29ff986dd">OpenMS::FeaFiModule::SpectrumType</a></div><div class="ttdeci">MapType::SpectrumType SpectrumType</div><div class="ttdoc">Input spectrum type. </div><div class="ttdef"><b>Definition:</b> FeaFiModule.h:166</div></div>
<div class="ttc" id="structOpenMS_1_1Internal_1_1RtIterator_html_a3a08b12523ea66ba7871e9bc5c6ce1b0"><div class="ttname"><a href="structOpenMS_1_1Internal_1_1RtIterator.html#a3a08b12523ea66ba7871e9bc5c6ce1b0">OpenMS::Internal::RtIterator::module_</a></div><div class="ttdeci">const FeaFiModuleType * module_</div><div class="ttdef"><b>Definition:</b> FeaFiModule.h:147</div></div>
<div class="ttc" id="FeatureMap_8h_html"><div class="ttname"><a href="FeatureMap_8h.html">FeatureMap.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1FeaFiModule_html_a21ea3968c35235b6b3cd78a2190280d9"><div class="ttname"><a href="classOpenMS_1_1FeaFiModule.html#a21ea3968c35235b6b3cd78a2190280d9">OpenMS::FeaFiModule::FeatureMapType</a></div><div class="ttdeci">FeatureMap< FeatureType > FeatureMapType</div><div class="ttdoc">Output feature map type. </div><div class="ttdef"><b>Definition:</b> FeaFiModule.h:162</div></div>
<div class="ttc" id="structOpenMS_1_1Internal_1_1IntensityIterator_html_a3a08b12523ea66ba7871e9bc5c6ce1b0"><div class="ttname"><a href="structOpenMS_1_1Internal_1_1IntensityIterator.html#a3a08b12523ea66ba7871e9bc5c6ce1b0">OpenMS::Internal::IntensityIterator::module_</a></div><div class="ttdeci">const FeaFiModuleType * module_</div><div class="ttdef"><b>Definition:</b> FeaFiModule.h:103</div></div>
<div class="ttc" id="structOpenMS_1_1Internal_1_1IntensityLess_html_a9baf7271d6c179b931d60d9f96e9e215"><div class="ttname"><a href="structOpenMS_1_1Internal_1_1IntensityLess.html#a9baf7271d6c179b931d60d9f96e9e215">OpenMS::Internal::IntensityLess::operator()</a></div><div class="ttdeci">bool operator()(const typename FeatureFinderDefs::IndexPair &left, const typename FeatureFinderDefs::IndexPair &right) const </div><div class="ttdoc">Compare with respect to intensity. </div><div class="ttdef"><b>Definition:</b> FeaFiModule.h:72</div></div>
<div class="ttc" id="classOpenMS_1_1FeaFiModule_html_ad3fe3d27b98fcd12d996b358e30723fa"><div class="ttname"><a href="classOpenMS_1_1FeaFiModule.html#ad3fe3d27b98fcd12d996b358e30723fa">OpenMS::FeaFiModule::FeaFiModule</a></div><div class="ttdeci">FeaFiModule(const MSExperiment< PeakType > *map, FeatureMap< FeatureType > *features, FeatureFinder *ff)</div><div class="ttdoc">Constructor. </div><div class="ttdef"><b>Definition:</b> FeaFiModule.h:173</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>
|
