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
|
<HTML>
<HEAD>
<TITLE>FeatureFinder Class Reference</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="namespaceOpenMS.html">OpenMS</a></li><li class="navelem"><a class="el" href="classOpenMS_1_1FeatureFinder.html">FeatureFinder</a></li> </ul>
</div>
</div><!-- top -->
<div class="header">
<div class="summary">
<a href="#pub-methods">Public Member Functions</a> |
<a href="#pro-attribs">Protected Attributes</a> |
<a href="classOpenMS_1_1FeatureFinder-members.html">List of all members</a> </div>
<div class="headertitle">
<div class="title">FeatureFinder Class Reference<div class="ingroups"><a class="el" href="group__FeatureFinder.html">FeatureFinder</a></div></div> </div>
</div><!--header-->
<div class="contents">
<p>The main feature finder class.
<a href="classOpenMS_1_1FeatureFinder.html#details">More...</a></p>
<p><code>#include <<a class="el" href="FeatureFinder_8h_source.html">OpenMS/TRANSFORMATIONS/FEATUREFINDER/FeatureFinder.h</a>></code></p>
<div class="dynheader">
Inheritance diagram for FeatureFinder:</div>
<div class="dyncontent">
<div class="center">
<img src="classOpenMS_1_1FeatureFinder.png" usemap="#FeatureFinder_map" alt=""/>
<map id="FeatureFinder_map" name="FeatureFinder_map">
<area href="classOpenMS_1_1ProgressLogger.html" title="Base class for all classes that want to report their progess. " alt="ProgressLogger" shape="rect" coords="0,0,119,24"/>
<area href="structOpenMS_1_1FeatureFinderDefs.html" title="The purpose of this struct is to provide definitions of classes and typedefs which are used throughou..." alt="FeatureFinderDefs" shape="rect" coords="129,0,248,24"/>
</map>
</div></div>
<table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
Public Member Functions</h2></td></tr>
<tr class="memitem:a88ac1a1518d9906398f0359255c289d6"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinder.html#a88ac1a1518d9906398f0359255c289d6">FeatureFinder</a> ()</td></tr>
<tr class="memdesc:a88ac1a1518d9906398f0359255c289d6"><td class="mdescLeft"> </td><td class="mdescRight">Default constructor. <a href="#a88ac1a1518d9906398f0359255c289d6">More...</a><br/></td></tr>
<tr class="separator:a88ac1a1518d9906398f0359255c289d6"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a1fdb9a841205a8348b337a69fde5c866"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinder.html#a1fdb9a841205a8348b337a69fde5c866">~FeatureFinder</a> ()</td></tr>
<tr class="memdesc:a1fdb9a841205a8348b337a69fde5c866"><td class="mdescLeft"> </td><td class="mdescRight">Destructor. <a href="#a1fdb9a841205a8348b337a69fde5c866">More...</a><br/></td></tr>
<tr class="separator:a1fdb9a841205a8348b337a69fde5c866"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a001d4adf21652ff6cdd58efe56e4fb1c"><td class="memTemplParams" colspan="2">template<class PeakType , class FeatureType > </td></tr>
<tr class="memitem:a001d4adf21652ff6cdd58efe56e4fb1c"><td class="memTemplItemLeft" align="right" valign="top">void </td><td class="memTemplItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinder.html#a001d4adf21652ff6cdd58efe56e4fb1c">run</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &algorithm_name, <a class="el" href="classOpenMS_1_1MSExperiment.html">MSExperiment</a>< <a class="el" href="namespaceOpenMS.html#a013338b7bdbb5c3b4c78666656070e23">PeakType</a> > &input_map, <a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a>< FeatureType > &features, const <a class="el" href="classOpenMS_1_1Param.html">Param</a> &param, const <a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a>< FeatureType > &seeds)</td></tr>
<tr class="memdesc:a001d4adf21652ff6cdd58efe56e4fb1c"><td class="mdescLeft"> </td><td class="mdescRight">Executes the <a class="el" href="classOpenMS_1_1FeatureFinder.html" title="The main feature finder class. ">FeatureFinder</a> using the given algorithm. <a href="#a001d4adf21652ff6cdd58efe56e4fb1c">More...</a><br/></td></tr>
<tr class="separator:a001d4adf21652ff6cdd58efe56e4fb1c"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a91adbb58dfeb79d2b5d78c1047f406c9"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="structOpenMS_1_1FeatureFinderDefs.html#a3f3de3e0d751949b8d0b60ffb302944a">Flag</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinder.html#a91adbb58dfeb79d2b5d78c1047f406c9">getPeakFlag</a> (const <a class="el" href="structOpenMS_1_1FeatureFinderDefs.html#aaee0bfd850887fdc58115cead9e9b8b9">IndexPair</a> &index) const </td></tr>
<tr class="memdesc:a91adbb58dfeb79d2b5d78c1047f406c9"><td class="mdescLeft"> </td><td class="mdescRight">Returns a non-mutable reference to a peak flag. <a href="#a91adbb58dfeb79d2b5d78c1047f406c9">More...</a><br/></td></tr>
<tr class="separator:a91adbb58dfeb79d2b5d78c1047f406c9"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:afab28fdfdaf463394002ddb7735102bf"><td class="memItemLeft" align="right" valign="top"><a class="el" href="structOpenMS_1_1FeatureFinderDefs.html#a3f3de3e0d751949b8d0b60ffb302944a">Flag</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinder.html#afab28fdfdaf463394002ddb7735102bf">getPeakFlag</a> (const <a class="el" href="structOpenMS_1_1FeatureFinderDefs.html#aaee0bfd850887fdc58115cead9e9b8b9">IndexPair</a> &index)</td></tr>
<tr class="memdesc:afab28fdfdaf463394002ddb7735102bf"><td class="mdescLeft"> </td><td class="mdescRight">Returns mutable reference to a peak flag. <a href="#afab28fdfdaf463394002ddb7735102bf">More...</a><br/></td></tr>
<tr class="separator:afab28fdfdaf463394002ddb7735102bf"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a65e60a513a7e5c3ff6b1223cca9a0bf0"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1Param.html">Param</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinder.html#a65e60a513a7e5c3ff6b1223cca9a0bf0">getParameters</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &algorithm_name) const </td></tr>
<tr class="memdesc:a65e60a513a7e5c3ff6b1223cca9a0bf0"><td class="mdescLeft"> </td><td class="mdescRight">Returns the default parameters for the algorithm with name <code>algorithm_name</code>. <a href="#a65e60a513a7e5c3ff6b1223cca9a0bf0">More...</a><br/></td></tr>
<tr class="separator:a65e60a513a7e5c3ff6b1223cca9a0bf0"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="inherit_header pub_methods_classOpenMS_1_1ProgressLogger"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_classOpenMS_1_1ProgressLogger')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a></td></tr>
<tr class="memitem:a2a106011aec95b2013d7a545f2063d01 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a2a106011aec95b2013d7a545f2063d01">ProgressLogger</a> ()</td></tr>
<tr class="memdesc:a2a106011aec95b2013d7a545f2063d01 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="mdescLeft"> </td><td class="mdescRight">Constructor. <a href="#a2a106011aec95b2013d7a545f2063d01">More...</a><br/></td></tr>
<tr class="separator:a2a106011aec95b2013d7a545f2063d01 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a19c882d907f90f7f88c7436d82cd2a13 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a19c882d907f90f7f88c7436d82cd2a13">~ProgressLogger</a> ()</td></tr>
<tr class="memdesc:a19c882d907f90f7f88c7436d82cd2a13 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="mdescLeft"> </td><td class="mdescRight">Destructor. <a href="#a19c882d907f90f7f88c7436d82cd2a13">More...</a><br/></td></tr>
<tr class="separator:a19c882d907f90f7f88c7436d82cd2a13 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:acc3538c5284777d8702ccaefeb61e74c inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#acc3538c5284777d8702ccaefeb61e74c">setLogType</a> (<a class="el" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87c">LogType</a> type) const </td></tr>
<tr class="memdesc:acc3538c5284777d8702ccaefeb61e74c inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="mdescLeft"> </td><td class="mdescRight">Sets the progress log that should be used. The default type is NONE! <a href="#acc3538c5284777d8702ccaefeb61e74c">More...</a><br/></td></tr>
<tr class="separator:acc3538c5284777d8702ccaefeb61e74c inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a67024cdd5c34ec571baecabd8f783310 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87c">LogType</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a67024cdd5c34ec571baecabd8f783310">getLogType</a> () const </td></tr>
<tr class="memdesc:a67024cdd5c34ec571baecabd8f783310 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="mdescLeft"> </td><td class="mdescRight">Returns the type of progress log being used. <a href="#a67024cdd5c34ec571baecabd8f783310">More...</a><br/></td></tr>
<tr class="separator:a67024cdd5c34ec571baecabd8f783310 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:af1c45ecd71b5041b70319249e8e73591 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#af1c45ecd71b5041b70319249e8e73591">startProgress</a> (<a class="el" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> begin, <a class="el" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> end, const <a class="el" href="classOpenMS_1_1String.html">String</a> &label) const </td></tr>
<tr class="memdesc:af1c45ecd71b5041b70319249e8e73591 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="mdescLeft"> </td><td class="mdescRight">Initializes the progress display. <a href="#af1c45ecd71b5041b70319249e8e73591">More...</a><br/></td></tr>
<tr class="separator:af1c45ecd71b5041b70319249e8e73591 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a8852277abd03220cc7b80d6c1bed6fed inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a8852277abd03220cc7b80d6c1bed6fed">setProgress</a> (<a class="el" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> value) const </td></tr>
<tr class="memdesc:a8852277abd03220cc7b80d6c1bed6fed inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="mdescLeft"> </td><td class="mdescRight">Sets the current progress. <a href="#a8852277abd03220cc7b80d6c1bed6fed">More...</a><br/></td></tr>
<tr class="separator:a8852277abd03220cc7b80d6c1bed6fed inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a1cc1012b0cdaea97f58d571af1ff45de inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a1cc1012b0cdaea97f58d571af1ff45de">endProgress</a> () const </td></tr>
<tr class="memdesc:a1cc1012b0cdaea97f58d571af1ff45de inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="mdescLeft"> </td><td class="mdescRight">Ends the progress display. <a href="#a1cc1012b0cdaea97f58d571af1ff45de">More...</a><br/></td></tr>
<tr class="separator:a1cc1012b0cdaea97f58d571af1ff45de inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pro-attribs"></a>
Protected Attributes</h2></td></tr>
<tr class="memitem:a9d6dd782a9b8b7ced5a44f7bc29f5ecc"><td class="memItemLeft" align="right" valign="top">std::vector< std::vector< <a class="el" href="structOpenMS_1_1FeatureFinderDefs.html#a3f3de3e0d751949b8d0b60ffb302944a">Flag</a> > > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinder.html#a9d6dd782a9b8b7ced5a44f7bc29f5ecc">flags_</a></td></tr>
<tr class="memdesc:a9d6dd782a9b8b7ced5a44f7bc29f5ecc"><td class="mdescLeft"> </td><td class="mdescRight">Container for flags attached to input data. <a href="#a9d6dd782a9b8b7ced5a44f7bc29f5ecc">More...</a><br/></td></tr>
<tr class="separator:a9d6dd782a9b8b7ced5a44f7bc29f5ecc"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="inherit_header pro_attribs_classOpenMS_1_1ProgressLogger"><td colspan="2" onclick="javascript:toggleInherit('pro_attribs_classOpenMS_1_1ProgressLogger')"><img src="closed.png" alt="-"/> Protected Attributes inherited from <a class="el" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a></td></tr>
<tr class="memitem:a7c691d7de2a43bc5606e96cb15da3641 inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87c">LogType</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a7c691d7de2a43bc5606e96cb15da3641">type_</a></td></tr>
<tr class="separator:a7c691d7de2a43bc5606e96cb15da3641 inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a56589612e0e4164bf80c3918a087d05a inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a56589612e0e4164bf80c3918a087d05a">begin_</a></td></tr>
<tr class="separator:a56589612e0e4164bf80c3918a087d05a inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a0c749bf4e621699b7a5c45ae22c2fa90 inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a0c749bf4e621699b7a5c45ae22c2fa90">end_</a></td></tr>
<tr class="separator:a0c749bf4e621699b7a5c45ae22c2fa90 inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aec57b26e143202dc119a41592e075932 inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#aec57b26e143202dc119a41592e075932">value_</a></td></tr>
<tr class="separator:aec57b26e143202dc119a41592e075932 inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a76072b3919abcf01141ba68da8a001fd inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">QProgressDialog * </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a76072b3919abcf01141ba68da8a001fd">dlg_</a></td></tr>
<tr class="separator:a76072b3919abcf01141ba68da8a001fd inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a6d9750520313ea7f843d7a49cb2e9e5f inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1StopWatch.html">StopWatch</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a6d9750520313ea7f843d7a49cb2e9e5f">stop_watch_</a></td></tr>
<tr class="separator:a6d9750520313ea7f843d7a49cb2e9e5f inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a79bacf60c4109d7517590441c7f85f9c inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">time_t </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a79bacf60c4109d7517590441c7f85f9c">last_invoke_</a></td></tr>
<tr class="separator:a79bacf60c4109d7517590441c7f85f9c inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="inherited"></a>
Additional Inherited Members</h2></td></tr>
<tr class="inherit_header pub_types_classOpenMS_1_1ProgressLogger"><td colspan="2" onclick="javascript:toggleInherit('pub_types_classOpenMS_1_1ProgressLogger')"><img src="closed.png" alt="-"/> Public Types inherited from <a class="el" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a></td></tr>
<tr class="memitem:af67907baa897e9fb84df0cb89795b87c inherit pub_types_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">enum  </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87c">LogType</a> { <a class="el" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87ca3ab34dd50405af2d5a62627d572f7860">CMD</a>,
<a class="el" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87ca73c6901c7c648a6a735770bc038bb26a">GUI</a>,
<a class="el" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87cac157bdf0b85a40d2619cbc8bc1ae5fe2">NONE</a>
}</td></tr>
<tr class="memdesc:af67907baa897e9fb84df0cb89795b87c"><td class="mdescLeft"> </td><td class="mdescRight">Possible log types. <a href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87c">More...</a><br/></td></tr>
<tr class="separator:af67907baa897e9fb84df0cb89795b87c inherit pub_types_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="inherit_header pub_types_structOpenMS_1_1FeatureFinderDefs"><td colspan="2" onclick="javascript:toggleInherit('pub_types_structOpenMS_1_1FeatureFinderDefs')"><img src="closed.png" alt="-"/> Public Types inherited from <a class="el" href="structOpenMS_1_1FeatureFinderDefs.html">FeatureFinderDefs</a></td></tr>
<tr class="memitem:a3f3de3e0d751949b8d0b60ffb302944a inherit pub_types_structOpenMS_1_1FeatureFinderDefs"><td class="memItemLeft" align="right" valign="top">enum  </td><td class="memItemRight" valign="bottom"><a class="el" href="structOpenMS_1_1FeatureFinderDefs.html#a3f3de3e0d751949b8d0b60ffb302944a">Flag</a> { <a class="el" href="structOpenMS_1_1FeatureFinderDefs.html#a3f3de3e0d751949b8d0b60ffb302944aaa09b651ef326a9d8efcee5cc5b720ab4">UNUSED</a>,
<a class="el" href="structOpenMS_1_1FeatureFinderDefs.html#a3f3de3e0d751949b8d0b60ffb302944aa1e780c62cb3fd2edcac39f739bbe6f6c">USED</a>
}</td></tr>
<tr class="memdesc:a3f3de3e0d751949b8d0b60ffb302944a"><td class="mdescLeft"> </td><td class="mdescRight">Flags that indicate if a peak is already used in a feature. <a href="structOpenMS_1_1FeatureFinderDefs.html#a3f3de3e0d751949b8d0b60ffb302944a">More...</a><br/></td></tr>
<tr class="separator:a3f3de3e0d751949b8d0b60ffb302944a inherit pub_types_structOpenMS_1_1FeatureFinderDefs"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aaee0bfd850887fdc58115cead9e9b8b9 inherit pub_types_structOpenMS_1_1FeatureFinderDefs"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="structOpenMS_1_1IsotopeCluster.html#a0cab124671a3ada269f0553e1c8934da">IsotopeCluster::IndexPair</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="structOpenMS_1_1FeatureFinderDefs.html#aaee0bfd850887fdc58115cead9e9b8b9">IndexPair</a></td></tr>
<tr class="memdesc:aaee0bfd850887fdc58115cead9e9b8b9 inherit pub_types_structOpenMS_1_1FeatureFinderDefs"><td class="mdescLeft"> </td><td class="mdescRight">Index to peak consisting of two UInts (scan index / peak index) <a href="#aaee0bfd850887fdc58115cead9e9b8b9">More...</a><br/></td></tr>
<tr class="separator:aaee0bfd850887fdc58115cead9e9b8b9 inherit pub_types_structOpenMS_1_1FeatureFinderDefs"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:af01a99958d0b18999737158daf8820ac inherit pub_types_structOpenMS_1_1FeatureFinderDefs"><td class="memItemLeft" align="right" valign="top">typedef <br class="typebreak"/>
<a class="el" href="structOpenMS_1_1IsotopeCluster_1_1ChargedIndexSet.html">IsotopeCluster::ChargedIndexSet</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="structOpenMS_1_1FeatureFinderDefs.html#af01a99958d0b18999737158daf8820ac">ChargedIndexSet</a></td></tr>
<tr class="memdesc:af01a99958d0b18999737158daf8820ac inherit pub_types_structOpenMS_1_1FeatureFinderDefs"><td class="mdescLeft"> </td><td class="mdescRight">Index to peak consisting of two UInts (scan index / peak index) with charge information. <a href="#af01a99958d0b18999737158daf8820ac">More...</a><br/></td></tr>
<tr class="separator:af01a99958d0b18999737158daf8820ac inherit pub_types_structOpenMS_1_1FeatureFinderDefs"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:af7439235b89a75354a2e87350e36834f inherit pub_types_structOpenMS_1_1FeatureFinderDefs"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="structOpenMS_1_1IsotopeCluster.html#aed4049efd4228c847ab300ac4c466eca">IsotopeCluster::IndexSet</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="structOpenMS_1_1FeatureFinderDefs.html#af7439235b89a75354a2e87350e36834f">IndexSet</a></td></tr>
<tr class="memdesc:af7439235b89a75354a2e87350e36834f inherit pub_types_structOpenMS_1_1FeatureFinderDefs"><td class="mdescLeft"> </td><td class="mdescRight">A set of peak indices. <a href="#af7439235b89a75354a2e87350e36834f">More...</a><br/></td></tr>
<tr class="separator:af7439235b89a75354a2e87350e36834f inherit pub_types_structOpenMS_1_1FeatureFinderDefs"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="inherit_header pro_static_attribs_classOpenMS_1_1ProgressLogger"><td colspan="2" onclick="javascript:toggleInherit('pro_static_attribs_classOpenMS_1_1ProgressLogger')"><img src="closed.png" alt="-"/> Static Protected Attributes inherited from <a class="el" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a></td></tr>
<tr class="memitem:a94eb3ef5ef94b83eb348dd00a2b53119 inherit pro_static_attribs_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">static int </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a94eb3ef5ef94b83eb348dd00a2b53119">recursion_depth_</a></td></tr>
<tr class="separator:a94eb3ef5ef94b83eb348dd00a2b53119 inherit pro_static_attribs_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
</table>
<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><p>The main feature finder class. </p>
<ul>
<li>Stores the flags for (indices of) data points ("used", "unused")</li>
<li>The algorithm itself is a factory product (derived from <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithm.html" title="Abstract base class for FeatureFinder algorithms. ">FeatureFinderAlgorithm</a>)</li>
<li>The main method is <a class="el" href="classOpenMS_1_1FeatureFinder.html#a001d4adf21652ff6cdd58efe56e4fb1c" title="Executes the FeatureFinder using the given algorithm. ">run()</a>, which is a template so that we can deal with different types of input and output</li>
<li>The <a class="el" href="classOpenMS_1_1FeatureFinder.html#a001d4adf21652ff6cdd58efe56e4fb1c" title="Executes the FeatureFinder using the given algorithm. ">run()</a> method takes five arguments: algorithm_name, input_map, output, parameters, seeds</li>
</ul>
</div><h2 class="groupheader">Constructor & Destructor Documentation</h2>
<a class="anchor" id="a88ac1a1518d9906398f0359255c289d6"></a>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname"><a class="el" href="classOpenMS_1_1FeatureFinder.html">FeatureFinder</a> </td>
<td>(</td>
<td class="paramname"></td><td>)</td>
<td></td>
</tr>
</table>
</div><div class="memdoc">
<p>Default constructor. </p>
</div>
</div>
<a class="anchor" id="a1fdb9a841205a8348b337a69fde5c866"></a>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">virtual ~<a class="el" href="classOpenMS_1_1FeatureFinder.html">FeatureFinder</a> </td>
<td>(</td>
<td class="paramname"></td><td>)</td>
<td></td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel">virtual</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>Destructor. </p>
</div>
</div>
<h2 class="groupheader">Member Function Documentation</h2>
<a class="anchor" id="a65e60a513a7e5c3ff6b1223cca9a0bf0"></a>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname"><a class="el" href="classOpenMS_1_1Param.html">Param</a> getParameters </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="classOpenMS_1_1String.html">String</a> & </td>
<td class="paramname"><em>algorithm_name</em></td><td>)</td>
<td> const</td>
</tr>
</table>
</div><div class="memdoc">
<p>Returns the default parameters for the algorithm with name <code>algorithm_name</code>. </p>
</div>
</div>
<a class="anchor" id="a91adbb58dfeb79d2b5d78c1047f406c9"></a>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">const <a class="el" href="structOpenMS_1_1FeatureFinderDefs.html#a3f3de3e0d751949b8d0b60ffb302944a">Flag</a>& getPeakFlag </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="structOpenMS_1_1FeatureFinderDefs.html#aaee0bfd850887fdc58115cead9e9b8b9">IndexPair</a> & </td>
<td class="paramname"><em>index</em></td><td>)</td>
<td> const</td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel">inline</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>Returns a non-mutable reference to a peak flag. </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1SimpleExtender.html#a8597c0a5982f48f9a8387e286b0251b0">SimpleExtender< PeakType, FeatureType >::checkNeighbour_()</a>, <a class="el" href="classOpenMS_1_1SimpleExtender.html#a1139a06b7cf1886d1977e5afcfddfea6">SimpleExtender< PeakType, FeatureType >::extend()</a>, <a class="el" href="classOpenMS_1_1ModelFitter.html#a9a599157dfa0c832cf50f5596342c73e">ModelFitter< PeakType, FeatureType >::fit()</a>, <a class="el" href="classOpenMS_1_1SimpleSeeder.html#a9101eb2633f34b26a1436b3d8e1e7522">SimpleSeeder< PeakType, FeatureType >::nextSeed()</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmSimplest.html#a72fcb26a14f6beb1c3fbace9ab3e7dbb">FeatureFinderAlgorithmSimplest< PeakType, FeatureType >::run()</a>, and <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmSimple.html#a72fcb26a14f6beb1c3fbace9ab3e7dbb">FeatureFinderAlgorithmSimple< PeakType, FeatureType >::run()</a>.</p>
</div>
</div>
<a class="anchor" id="afab28fdfdaf463394002ddb7735102bf"></a>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname"><a class="el" href="structOpenMS_1_1FeatureFinderDefs.html#a3f3de3e0d751949b8d0b60ffb302944a">Flag</a>& getPeakFlag </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="structOpenMS_1_1FeatureFinderDefs.html#aaee0bfd850887fdc58115cead9e9b8b9">IndexPair</a> & </td>
<td class="paramname"><em>index</em></td><td>)</td>
<td></td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel">inline</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>Returns mutable reference to a peak flag. </p>
</div>
</div>
<a class="anchor" id="a001d4adf21652ff6cdd58efe56e4fb1c"></a>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">void run </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="classOpenMS_1_1String.html">String</a> & </td>
<td class="paramname"><em>algorithm_name</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="classOpenMS_1_1MSExperiment.html">MSExperiment</a>< <a class="el" href="namespaceOpenMS.html#a013338b7bdbb5c3b4c78666656070e23">PeakType</a> > & </td>
<td class="paramname"><em>input_map</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a>< FeatureType > & </td>
<td class="paramname"><em>features</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">const <a class="el" href="classOpenMS_1_1Param.html">Param</a> & </td>
<td class="paramname"><em>param</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">const <a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a>< FeatureType > & </td>
<td class="paramname"><em>seeds</em> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td>
</tr>
</table>
</div><div class="memdoc">
<p>Executes the <a class="el" href="classOpenMS_1_1FeatureFinder.html" title="The main feature finder class. ">FeatureFinder</a> using the given algorithm. </p>
<p>There are several constraints for the <code>input_map</code>. They are tested before the algorithm starts. It must only contain MS 1 level scans and you have to call updateRanges() before passing it to this method. The input map is sorted by RT & m/z if thats not the case. Furthermore we throw an <a class="el" href="namespaceOpenMS_1_1Exception.html" title="Exception namespace ">Exception</a> if the data contains negative m/z values, as this will disturb most algorithms.</p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">algorithm_name</td><td>Name of the feature finding algorithm to use </td></tr>
<tr><td class="paramname">input_map</td><td>Input peak map </td></tr>
<tr><td class="paramname">features</td><td>Output feature map </td></tr>
<tr><td class="paramname">param</td><td>Algorithm parameters </td></tr>
<tr><td class="paramname">seeds</td><td>List of seeds to use</td></tr>
</table>
</dd>
</dl>
<p>Implemented in <a class="el" href="FeatureFinder__impl_8h.html">FeatureFinder_impl.h</a> </p>
<dl class="todo"><dt><b><a class="el" href="todo.html#_todo000019">Todo:</a></b></dt><dd>that happens sometimes using IsotopeWaveletFeatureFinder (Rene, Marc, Andreas, Clemens) </dd></dl>
<p>References <a class="el" href="classOpenMS_1_1MSExperiment.html#a2387033802383edbdc95f9bbb12a707e">MSExperiment< PeakT, ChromatogramPeakT >::begin()</a>, <a class="el" href="classOpenMS_1_1FeatureMap.html#a7b5660c6199fa9d5fef65974c7e3e733">FeatureMap< FeatureT >::clear()</a>, <a class="el" href="classOpenMS_1_1MSExperiment.html#ac6e61de369e994009e36f344f99c15ad">MSExperiment< PeakT, ChromatogramPeakT >::empty()</a>, <a class="el" href="classOpenMS_1_1FeatureFinder.html#a9d6dd782a9b8b7ced5a44f7bc29f5ecc">FeatureFinder::flags_</a>, <a class="el" href="classOpenMS_1_1MSExperiment.html#a02fccfed86a20f8bd0f6b98c23fadb2e">MSExperiment< PeakT, ChromatogramPeakT >::getChromatograms()</a>, <a class="el" href="classOpenMS_1_1MSExperiment.html#adbc1e31b95b2364ef4b3b1ba94b0aa8d">MSExperiment< PeakT, ChromatogramPeakT >::getMSLevels()</a>, <a class="el" href="classOpenMS_1_1MSExperiment.html#aac09407a6369916d487f3a83527b8398">MSExperiment< PeakT, ChromatogramPeakT >::getSize()</a>, <a class="el" href="classOpenMS_1_1MSExperiment.html#a50d19782103ccc00edaabfba88dd2598">MSExperiment< PeakT, ChromatogramPeakT >::isSorted()</a>, <a class="el" href="LogStream_8h.html#aea3f57d6dcc5b4ac957e2679e87dde27">LOG_WARN</a>, <a class="el" href="classOpenMS_1_1MSExperiment.html#adb2f0f3e10754ca4dc7be677f15689a3">MSExperiment< PeakT, ChromatogramPeakT >::RTBegin()</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a18954417d3124a8095783ea13dc6d00b">FeatureFinderAlgorithm< PeakType, FeatureType >::run()</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a7e594645b8460e600602bb64a8403537">FeatureFinderAlgorithm< PeakType, FeatureType >::setData()</a>, <a class="el" href="classOpenMS_1_1DefaultParamHandler.html#abc8067511cfc949ae942ea2b08588f81">DefaultParamHandler::setParameters()</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a683154793bbb12ab5d16db81209606b0">FeatureFinderAlgorithm< PeakType, FeatureType >::setSeeds()</a>, <a class="el" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">MSExperiment< PeakT, ChromatogramPeakT >::size()</a>, <a class="el" href="classOpenMS_1_1MSExperiment.html#aa679772c8c6b65183102bc220ebe7870">MSExperiment< PeakT, ChromatogramPeakT >::sortChromatograms()</a>, <a class="el" href="classOpenMS_1_1MSExperiment.html#ac518a80bea4f92fd700b235a12146658">MSExperiment< PeakT, ChromatogramPeakT >::sortSpectra()</a>, and <a class="el" href="structOpenMS_1_1FeatureFinderDefs.html#a3f3de3e0d751949b8d0b60ffb302944aaa09b651ef326a9d8efcee5cc5b720ab4">FeatureFinderDefs::UNUSED</a>.</p>
</div>
</div>
<h2 class="groupheader">Member Data Documentation</h2>
<a class="anchor" id="a9d6dd782a9b8b7ced5a44f7bc29f5ecc"></a>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">std::vector<std::vector<<a class="el" href="structOpenMS_1_1FeatureFinderDefs.html#a3f3de3e0d751949b8d0b60ffb302944a">Flag</a>> > flags_</td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel">protected</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>Container for flags attached to input data. </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1FeatureFinder.html#a001d4adf21652ff6cdd58efe56e4fb1c">FeatureFinder::run()</a>.</p>
</div>
</div>
</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 11:19:34 using doxygen 1.8.5</font></TD>
</TR>
</TABLE>
</BODY>
</HTML>
|
