File: ProteinIdentification_8h_source.html

package info (click to toggle)
openms 1.11.1-5
  • links: PTS, VCS
  • area: main
  • in suites: jessie, jessie-kfreebsd
  • size: 436,688 kB
  • ctags: 150,907
  • sloc: cpp: 387,126; xml: 71,547; python: 7,764; ansic: 2,626; php: 2,499; sql: 737; ruby: 342; sh: 325; makefile: 128
file content (296 lines) | stat: -rw-r--r-- 66,954 bytes parent folder | download 
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
 
<HTML>
<HEAD>
<TITLE>ProteinIdentification.h Source File</TITLE>
<LINK HREF="doxygen.css" REL="stylesheet" TYPE="text/css">
<LINK HREF="style_ini.css" REL="stylesheet" TYPE="text/css">
</HEAD>
<BODY BGCOLOR="#FFFFFF">
<A href="index.html">Home</A> &nbsp;&middot;
<A href="classes.html">Classes</A> &nbsp;&middot;
<A href="annotated.html">Annotated Classes</A> &nbsp;&middot;
<A href="modules.html">Modules</A> &nbsp;&middot;
<A href="functions_func.html">Members</A> &nbsp;&middot;
<A href="namespaces.html">Namespaces</A> &nbsp;&middot;
<A href="pages.html">Related Pages</A>
<HR style="height:1px; border:none; border-top:1px solid #c0c0c0;">
<!-- Generated by Doxygen 1.8.5 -->
<div id="nav-path" class="navpath">
  <ul>
<li class="navelem"><a class="el" href="dir_e770f0cf77e550adde3f44739ef529fe.html">include</a></li><li class="navelem"><a class="el" href="dir_6a63c4937d4da007e55fff5dcf71e0f8.html">OpenMS</a></li><li class="navelem"><a class="el" href="dir_2b6ad60ca9989d24a3386bb65e09c126.html">METADATA</a></li>  </ul>
</div>
</div><!-- top -->
<div class="header">
  <div class="headertitle">
<div class="title">ProteinIdentification.h</div>  </div>
</div><!--header-->
<div class="contents">
<a href="ProteinIdentification_8h.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno">    1</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00002"></a><span class="lineno">    2</span>&#160;<span class="comment">//                   OpenMS -- Open-Source Mass Spectrometry</span></div>
<div class="line"><a name="l00003"></a><span class="lineno">    3</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00004"></a><span class="lineno">    4</span>&#160;<span class="comment">// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,</span></div>
<div class="line"><a name="l00005"></a><span class="lineno">    5</span>&#160;<span class="comment">// ETH Zurich, and Freie Universitaet Berlin 2002-2013.</span></div>
<div class="line"><a name="l00006"></a><span class="lineno">    6</span>&#160;<span class="comment">//</span></div>
<div class="line"><a name="l00007"></a><span class="lineno">    7</span>&#160;<span class="comment">// This software is released under a three-clause BSD license:</span></div>
<div class="line"><a name="l00008"></a><span class="lineno">    8</span>&#160;<span class="comment">//  * Redistributions of source code must retain the above copyright</span></div>
<div class="line"><a name="l00009"></a><span class="lineno">    9</span>&#160;<span class="comment">//    notice, this list of conditions and the following disclaimer.</span></div>
<div class="line"><a name="l00010"></a><span class="lineno">   10</span>&#160;<span class="comment">//  * Redistributions in binary form must reproduce the above copyright</span></div>
<div class="line"><a name="l00011"></a><span class="lineno">   11</span>&#160;<span class="comment">//    notice, this list of conditions and the following disclaimer in the</span></div>
<div class="line"><a name="l00012"></a><span class="lineno">   12</span>&#160;<span class="comment">//    documentation and/or other materials provided with the distribution.</span></div>
<div class="line"><a name="l00013"></a><span class="lineno">   13</span>&#160;<span class="comment">//  * Neither the name of any author or any participating institution</span></div>
<div class="line"><a name="l00014"></a><span class="lineno">   14</span>&#160;<span class="comment">//    may be used to endorse or promote products derived from this software</span></div>
<div class="line"><a name="l00015"></a><span class="lineno">   15</span>&#160;<span class="comment">//    without specific prior written permission.</span></div>
<div class="line"><a name="l00016"></a><span class="lineno">   16</span>&#160;<span class="comment">// For a full list of authors, refer to the file AUTHORS.</span></div>
<div class="line"><a name="l00017"></a><span class="lineno">   17</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00018"></a><span class="lineno">   18</span>&#160;<span class="comment">// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS &quot;AS IS&quot;</span></div>
<div class="line"><a name="l00019"></a><span class="lineno">   19</span>&#160;<span class="comment">// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE</span></div>
<div class="line"><a name="l00020"></a><span class="lineno">   20</span>&#160;<span class="comment">// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE</span></div>
<div class="line"><a name="l00021"></a><span class="lineno">   21</span>&#160;<span class="comment">// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING</span></div>
<div class="line"><a name="l00022"></a><span class="lineno">   22</span>&#160;<span class="comment">// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,</span></div>
<div class="line"><a name="l00023"></a><span class="lineno">   23</span>&#160;<span class="comment">// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,</span></div>
<div class="line"><a name="l00024"></a><span class="lineno">   24</span>&#160;<span class="comment">// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;</span></div>
<div class="line"><a name="l00025"></a><span class="lineno">   25</span>&#160;<span class="comment">// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,</span></div>
<div class="line"><a name="l00026"></a><span class="lineno">   26</span>&#160;<span class="comment">// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR</span></div>
<div class="line"><a name="l00027"></a><span class="lineno">   27</span>&#160;<span class="comment">// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF</span></div>
<div class="line"><a name="l00028"></a><span class="lineno">   28</span>&#160;<span class="comment">// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</span></div>
<div class="line"><a name="l00029"></a><span class="lineno">   29</span>&#160;<span class="comment">//</span></div>
<div class="line"><a name="l00030"></a><span class="lineno">   30</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00031"></a><span class="lineno">   31</span>&#160;<span class="comment">// $Maintainer: Chris Bielow $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160;<span class="comment">// $Authors: Nico Pfeifer, Chris Bielow $</span></div>
<div class="line"><a name="l00033"></a><span class="lineno">   33</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00034"></a><span class="lineno">   34</span>&#160;</div>
<div class="line"><a name="l00035"></a><span class="lineno">   35</span>&#160;<span class="preprocessor">#ifndef OPENMS_METADATA_PROTEINIDENTIFICATION_H</span></div>
<div class="line"><a name="l00036"></a><span class="lineno">   36</span>&#160;<span class="preprocessor"></span><span class="preprocessor">#define OPENMS_METADATA_PROTEINIDENTIFICATION_H</span></div>
<div class="line"><a name="l00037"></a><span class="lineno">   37</span>&#160;<span class="preprocessor"></span></div>
<div class="line"><a name="l00038"></a><span class="lineno">   38</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="ProteinHit_8h.html">OpenMS/METADATA/ProteinHit.h</a>&gt;</span></div>
<div class="line"><a name="l00039"></a><span class="lineno">   39</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="MetaInfoInterface_8h.html">OpenMS/METADATA/MetaInfoInterface.h</a>&gt;</span></div>
<div class="line"><a name="l00040"></a><span class="lineno">   40</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="DateTime_8h.html">OpenMS/DATASTRUCTURES/DateTime.h</a>&gt;</span></div>
<div class="line"><a name="l00041"></a><span class="lineno">   41</span>&#160;</div>
<div class="line"><a name="l00042"></a><span class="lineno">   42</span>&#160;<span class="preprocessor">#include &lt;set&gt;</span></div>
<div class="line"><a name="l00043"></a><span class="lineno">   43</span>&#160;</div>
<div class="line"><a name="l00044"></a><span class="lineno">   44</span>&#160;<span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00045"></a><span class="lineno">   45</span>&#160;{</div>
<div class="line"><a name="l00046"></a><span class="lineno">   46</span>&#160;  <span class="keyword">class </span>PeptideIdentification;</div>
<div class="line"><a name="l00061"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ProteinIdentification.html">   61</a></span>&#160;  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a> :</div>
<div class="line"><a name="l00062"></a><span class="lineno">   62</span>&#160;    <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1MetaInfoInterface.html">MetaInfoInterface</a></div>
<div class="line"><a name="l00063"></a><span class="lineno">   63</span>&#160;  {</div>
<div class="line"><a name="l00064"></a><span class="lineno">   64</span>&#160;<span class="keyword">public</span>:</div>
<div class="line"><a name="l00066"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ProteinIdentification.html#a81790367e26e192b9eb9c7cad5f1730d">   66</a></span>&#160;    <span class="keyword">typedef</span> <a class="code" href="classOpenMS_1_1ProteinHit.html">ProteinHit</a> <a class="code" href="classOpenMS_1_1ProteinIdentification.html#a81790367e26e192b9eb9c7cad5f1730d">HitType</a>;</div>
<div class="line"><a name="l00067"></a><span class="lineno">   67</span>&#160;</div>
<div class="line"><a name="l00071"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ProteinIdentification_1_1ProteinGroup.html">   71</a></span>&#160;    <span class="keyword">struct </span><a class="code" href="structOpenMS_1_1ProteinIdentification_1_1ProteinGroup.html">ProteinGroup</a></div>
<div class="line"><a name="l00072"></a><span class="lineno">   72</span>&#160;    {</div>
<div class="line"><a name="l00074"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ProteinIdentification_1_1ProteinGroup.html#abb040260f33bb7404c0f2854d3a778d2">   74</a></span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="structOpenMS_1_1ProteinIdentification_1_1ProteinGroup.html#abb040260f33bb7404c0f2854d3a778d2">probability</a>;</div>
<div class="line"><a name="l00076"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ProteinIdentification_1_1ProteinGroup.html#a4920100bceeb1d49378a5d4370bba984">   76</a></span>&#160;      <a class="code" href="classOpenMS_1_1StringList.html">StringList</a> <a class="code" href="structOpenMS_1_1ProteinIdentification_1_1ProteinGroup.html#a4920100bceeb1d49378a5d4370bba984">accessions</a>;</div>
<div class="line"><a name="l00077"></a><span class="lineno">   77</span>&#160;</div>
<div class="line"><a name="l00078"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ProteinIdentification_1_1ProteinGroup.html#a2c5a181931200b0f5060c712f2e0568f">   78</a></span>&#160;      <a class="code" href="structOpenMS_1_1ProteinIdentification_1_1ProteinGroup.html#a2c5a181931200b0f5060c712f2e0568f">ProteinGroup</a>() :</div>
<div class="line"><a name="l00079"></a><span class="lineno">   79</span>&#160;        probability(0.0), accessions()</div>
<div class="line"><a name="l00080"></a><span class="lineno">   80</span>&#160;      {}</div>
<div class="line"><a name="l00081"></a><span class="lineno">   81</span>&#160;</div>
<div class="line"><a name="l00082"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ProteinIdentification_1_1ProteinGroup.html#aaa8621a18bcb39e46cbc54376b94b66e">   82</a></span>&#160;      <span class="keywordtype">bool</span> <a class="code" href="structOpenMS_1_1ProteinIdentification_1_1ProteinGroup.html#aaa8621a18bcb39e46cbc54376b94b66e">operator==</a>(<span class="keyword">const</span> <a class="code" href="structOpenMS_1_1ProteinIdentification_1_1ProteinGroup.html">ProteinGroup</a> rhs)<span class="keyword"> const</span></div>
<div class="line"><a name="l00083"></a><span class="lineno">   83</span>&#160;<span class="keyword">      </span>{</div>
<div class="line"><a name="l00084"></a><span class="lineno">   84</span>&#160;        <span class="keywordflow">return</span> probability == rhs.<a class="code" href="structOpenMS_1_1ProteinIdentification_1_1ProteinGroup.html#abb040260f33bb7404c0f2854d3a778d2">probability</a> &amp;&amp;</div>
<div class="line"><a name="l00085"></a><span class="lineno">   85</span>&#160;               accessions == rhs.<a class="code" href="structOpenMS_1_1ProteinIdentification_1_1ProteinGroup.html#a4920100bceeb1d49378a5d4370bba984">accessions</a>;</div>
<div class="line"><a name="l00086"></a><span class="lineno">   86</span>&#160;      }</div>
<div class="line"><a name="l00087"></a><span class="lineno">   87</span>&#160;</div>
<div class="line"><a name="l00088"></a><span class="lineno">   88</span>&#160;    };</div>
<div class="line"><a name="l00089"></a><span class="lineno">   89</span>&#160;</div>
<div class="line"><a name="l00091"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ProteinIdentification.html#a5431b65220b7ad71b5e8768876ee3e53">   91</a></span>&#160;    <span class="keyword">enum</span> <a class="code" href="classOpenMS_1_1ProteinIdentification.html#a5431b65220b7ad71b5e8768876ee3e53">PeakMassType</a></div>
<div class="line"><a name="l00092"></a><span class="lineno">   92</span>&#160;    {</div>
<div class="line"><a name="l00093"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ProteinIdentification.html#a5431b65220b7ad71b5e8768876ee3e53aba27416c974c26497ea0f4aa59fcf669">   93</a></span>&#160;      <a class="code" href="classOpenMS_1_1ProteinIdentification.html#a5431b65220b7ad71b5e8768876ee3e53aba27416c974c26497ea0f4aa59fcf669">MONOISOTOPIC</a>,</div>
<div class="line"><a name="l00094"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ProteinIdentification.html#a5431b65220b7ad71b5e8768876ee3e53ab6f2220659ddcb84a0622d4aa4e0b112">   94</a></span>&#160;      <a class="code" href="classOpenMS_1_1ProteinIdentification.html#a5431b65220b7ad71b5e8768876ee3e53ab6f2220659ddcb84a0622d4aa4e0b112">AVERAGE</a>,</div>
<div class="line"><a name="l00095"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ProteinIdentification.html#a5431b65220b7ad71b5e8768876ee3e53a2989e7c6c70923c0941b34c64517d012">   95</a></span>&#160;      SIZE_OF_PEAKMASSTYPE</div>
<div class="line"><a name="l00096"></a><span class="lineno">   96</span>&#160;    };</div>
<div class="line"><a name="l00098"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ProteinIdentification.html#a4dbe2d19835aa05a1c9c672fa254ef66">   98</a></span>&#160;    <span class="keyword">static</span> <span class="keyword">const</span> std::string NamesOfPeakMassType[SIZE_OF_PEAKMASSTYPE];</div>
<div class="line"><a name="l00099"></a><span class="lineno">   99</span>&#160;</div>
<div class="line"><a name="l00100"></a><span class="lineno">  100</span>&#160;</div>
<div class="line"><a name="l00101"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ProteinIdentification.html#ac1976fd756a09ae4e26fe6b32fcb396c">  101</a></span>&#160;    <span class="keyword">enum</span> <a class="code" href="classOpenMS_1_1ProteinIdentification.html#ac1976fd756a09ae4e26fe6b32fcb396c">DigestionEnzyme</a></div>
<div class="line"><a name="l00102"></a><span class="lineno">  102</span>&#160;    {</div>
<div class="line"><a name="l00103"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ProteinIdentification.html#ac1976fd756a09ae4e26fe6b32fcb396caa87783975563314a167c39f08f065bfd">  103</a></span>&#160;      <a class="code" href="classOpenMS_1_1ProteinIdentification.html#ac1976fd756a09ae4e26fe6b32fcb396caa87783975563314a167c39f08f065bfd">TRYPSIN</a>,</div>
<div class="line"><a name="l00104"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ProteinIdentification.html#ac1976fd756a09ae4e26fe6b32fcb396ca9cf5aedb487753ed0440ab34d94e1b33">  104</a></span>&#160;      <a class="code" href="classOpenMS_1_1ProteinIdentification.html#ac1976fd756a09ae4e26fe6b32fcb396ca9cf5aedb487753ed0440ab34d94e1b33">PEPSIN_A</a>,</div>
<div class="line"><a name="l00105"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ProteinIdentification.html#ac1976fd756a09ae4e26fe6b32fcb396ca3b5e4efa6ca1ae00905ead21fe2c1e73">  105</a></span>&#160;      <a class="code" href="classOpenMS_1_1ProteinIdentification.html#ac1976fd756a09ae4e26fe6b32fcb396ca3b5e4efa6ca1ae00905ead21fe2c1e73">PROTEASE_K</a>,</div>
<div class="line"><a name="l00106"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ProteinIdentification.html#ac1976fd756a09ae4e26fe6b32fcb396ca240cc037883891d0eb859a89530893ba">  106</a></span>&#160;      <a class="code" href="classOpenMS_1_1ProteinIdentification.html#ac1976fd756a09ae4e26fe6b32fcb396ca240cc037883891d0eb859a89530893ba">CHYMOTRYPSIN</a>,</div>
<div class="line"><a name="l00107"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ProteinIdentification.html#ac1976fd756a09ae4e26fe6b32fcb396ca8013b03f6b7f2d27796adf371a715a81">  107</a></span>&#160;      <a class="code" href="classOpenMS_1_1ProteinIdentification.html#ac1976fd756a09ae4e26fe6b32fcb396ca8013b03f6b7f2d27796adf371a715a81">NO_ENZYME</a>,</div>
<div class="line"><a name="l00108"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ProteinIdentification.html#ac1976fd756a09ae4e26fe6b32fcb396ca36a56e667bdbe75daa08c655e85ec49a">  108</a></span>&#160;      <a class="code" href="classOpenMS_1_1ProteinIdentification.html#ac1976fd756a09ae4e26fe6b32fcb396ca36a56e667bdbe75daa08c655e85ec49a">UNKNOWN_ENZYME</a>,</div>
<div class="line"><a name="l00109"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ProteinIdentification.html#ac1976fd756a09ae4e26fe6b32fcb396ca59ffc2972d48cca58d73eb79e40edf9f">  109</a></span>&#160;      SIZE_OF_DIGESTIONENZYME</div>
<div class="line"><a name="l00110"></a><span class="lineno">  110</span>&#160;    };</div>
<div class="line"><a name="l00112"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ProteinIdentification.html#a5712ee000feacb9e63b879136a658c57">  112</a></span>&#160;    <span class="keyword">static</span> <span class="keyword">const</span> std::string NamesOfDigestionEnzyme[SIZE_OF_DIGESTIONENZYME];</div>
<div class="line"><a name="l00113"></a><span class="lineno">  113</span>&#160;</div>
<div class="line"><a name="l00115"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html">  115</a></span>&#160;    <span class="keyword">struct </span><a class="code" href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html">SearchParameters</a> :</div>
<div class="line"><a name="l00116"></a><span class="lineno">  116</span>&#160;      <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1MetaInfoInterface.html">MetaInfoInterface</a></div>
<div class="line"><a name="l00117"></a><span class="lineno">  117</span>&#160;    {</div>
<div class="line"><a name="l00118"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html#ae525bb5a71aa3ae9d811588db4652c00">  118</a></span>&#160;      <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html#ae525bb5a71aa3ae9d811588db4652c00">db</a>;           </div>
<div class="line"><a name="l00119"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html#a0160159c20a3ab7cb61ce3b3091e0630">  119</a></span>&#160;      <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html#a0160159c20a3ab7cb61ce3b3091e0630">db_version</a>;           </div>
<div class="line"><a name="l00120"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html#a3ebfdcd6ebd0f389bf17b098a002c531">  120</a></span>&#160;      <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html#a3ebfdcd6ebd0f389bf17b098a002c531">taxonomy</a>;           </div>
<div class="line"><a name="l00121"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html#a6b3f6ef19caf97c201fba99444bf0663">  121</a></span>&#160;      <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html#a6b3f6ef19caf97c201fba99444bf0663">charges</a>;           </div>
<div class="line"><a name="l00122"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html#ae19806728daee03d5fc75855db1152d4">  122</a></span>&#160;      <a class="code" href="classOpenMS_1_1ProteinIdentification.html#a5431b65220b7ad71b5e8768876ee3e53">PeakMassType</a> <a class="code" href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html#ae19806728daee03d5fc75855db1152d4">mass_type</a>;           </div>
<div class="line"><a name="l00123"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html#a490c8a0c02713ba0b9fb56164a3b6887">  123</a></span>&#160;      std::vector&lt;String&gt; <a class="code" href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html#a490c8a0c02713ba0b9fb56164a3b6887">fixed_modifications</a>;           </div>
<div class="line"><a name="l00124"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html#adeefbd81d0184c04768844df11e5b979">  124</a></span>&#160;      std::vector&lt;String&gt; <a class="code" href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html#adeefbd81d0184c04768844df11e5b979">variable_modifications</a>;           </div>
<div class="line"><a name="l00125"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html#aef9bb017f25e4697cca5e2793f91b267">  125</a></span>&#160;      <a class="code" href="classOpenMS_1_1ProteinIdentification.html#ac1976fd756a09ae4e26fe6b32fcb396c">DigestionEnzyme</a> <a class="code" href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html#aef9bb017f25e4697cca5e2793f91b267">enzyme</a>;           </div>
<div class="line"><a name="l00126"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html#af70dd1b4c626832e04f0cc7fb04ac0e2">  126</a></span>&#160;      <a class="code" href="classunsigned_01int.html">UInt</a> <a class="code" href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html#af70dd1b4c626832e04f0cc7fb04ac0e2">missed_cleavages</a>;           </div>
<div class="line"><a name="l00127"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html#a59bf6893d99c96ed73c9699b2013fb76">  127</a></span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html#a59bf6893d99c96ed73c9699b2013fb76">peak_mass_tolerance</a>;           </div>
<div class="line"><a name="l00128"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html#a9665390243976d08d254b1d2e83876ad">  128</a></span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html#a9665390243976d08d254b1d2e83876ad">precursor_tolerance</a>;           </div>
<div class="line"><a name="l00129"></a><span class="lineno">  129</span>&#160;</div>
<div class="line"><a name="l00130"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html#a99f4b7d19585e6f1251cc9d8e1367f77">  130</a></span>&#160;      <a class="code" href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html#a99f4b7d19585e6f1251cc9d8e1367f77">SearchParameters</a>() :</div>
<div class="line"><a name="l00131"></a><span class="lineno">  131</span>&#160;        db(),</div>
<div class="line"><a name="l00132"></a><span class="lineno">  132</span>&#160;        db_version(),</div>
<div class="line"><a name="l00133"></a><span class="lineno">  133</span>&#160;        taxonomy(),</div>
<div class="line"><a name="l00134"></a><span class="lineno">  134</span>&#160;        charges(),</div>
<div class="line"><a name="l00135"></a><span class="lineno">  135</span>&#160;        mass_type(MONOISOTOPIC),</div>
<div class="line"><a name="l00136"></a><span class="lineno">  136</span>&#160;        fixed_modifications(),</div>
<div class="line"><a name="l00137"></a><span class="lineno">  137</span>&#160;        variable_modifications(),</div>
<div class="line"><a name="l00138"></a><span class="lineno">  138</span>&#160;        enzyme(UNKNOWN_ENZYME),</div>
<div class="line"><a name="l00139"></a><span class="lineno">  139</span>&#160;        missed_cleavages(0),</div>
<div class="line"><a name="l00140"></a><span class="lineno">  140</span>&#160;        peak_mass_tolerance(0.0),</div>
<div class="line"><a name="l00141"></a><span class="lineno">  141</span>&#160;        precursor_tolerance(0.0)</div>
<div class="line"><a name="l00142"></a><span class="lineno">  142</span>&#160;      {</div>
<div class="line"><a name="l00143"></a><span class="lineno">  143</span>&#160;      }</div>
<div class="line"><a name="l00144"></a><span class="lineno">  144</span>&#160;</div>
<div class="line"><a name="l00145"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html#afbafd06819616f82f69616ca89138c6e">  145</a></span>&#160;      <span class="keywordtype">bool</span> <a class="code" href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html#afbafd06819616f82f69616ca89138c6e">operator==</a>(<span class="keyword">const</span> <a class="code" href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html">SearchParameters</a> &amp; rhs)<span class="keyword"> const</span></div>
<div class="line"><a name="l00146"></a><span class="lineno">  146</span>&#160;<span class="keyword">      </span>{</div>
<div class="line"><a name="l00147"></a><span class="lineno">  147</span>&#160;        <span class="keywordflow">return</span> db == rhs.<a class="code" href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html#ae525bb5a71aa3ae9d811588db4652c00">db</a> &amp;&amp;</div>
<div class="line"><a name="l00148"></a><span class="lineno">  148</span>&#160;               db_version == rhs.<a class="code" href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html#a0160159c20a3ab7cb61ce3b3091e0630">db_version</a> &amp;&amp;</div>
<div class="line"><a name="l00149"></a><span class="lineno">  149</span>&#160;               taxonomy == rhs.<a class="code" href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html#a3ebfdcd6ebd0f389bf17b098a002c531">taxonomy</a> &amp;&amp;</div>
<div class="line"><a name="l00150"></a><span class="lineno">  150</span>&#160;               charges == rhs.<a class="code" href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html#a6b3f6ef19caf97c201fba99444bf0663">charges</a> &amp;&amp;</div>
<div class="line"><a name="l00151"></a><span class="lineno">  151</span>&#160;               mass_type == rhs.<a class="code" href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html#ae19806728daee03d5fc75855db1152d4">mass_type</a> &amp;&amp;</div>
<div class="line"><a name="l00152"></a><span class="lineno">  152</span>&#160;               fixed_modifications == rhs.<a class="code" href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html#a490c8a0c02713ba0b9fb56164a3b6887">fixed_modifications</a> &amp;&amp;</div>
<div class="line"><a name="l00153"></a><span class="lineno">  153</span>&#160;               variable_modifications == rhs.<a class="code" href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html#adeefbd81d0184c04768844df11e5b979">variable_modifications</a> &amp;&amp;</div>
<div class="line"><a name="l00154"></a><span class="lineno">  154</span>&#160;               enzyme == rhs.<a class="code" href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html#aef9bb017f25e4697cca5e2793f91b267">enzyme</a> &amp;&amp;</div>
<div class="line"><a name="l00155"></a><span class="lineno">  155</span>&#160;               missed_cleavages == rhs.<a class="code" href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html#af70dd1b4c626832e04f0cc7fb04ac0e2">missed_cleavages</a> &amp;&amp;</div>
<div class="line"><a name="l00156"></a><span class="lineno">  156</span>&#160;               peak_mass_tolerance == rhs.<a class="code" href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html#a59bf6893d99c96ed73c9699b2013fb76">peak_mass_tolerance</a> &amp;&amp;</div>
<div class="line"><a name="l00157"></a><span class="lineno">  157</span>&#160;               precursor_tolerance == rhs.<a class="code" href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html#a9665390243976d08d254b1d2e83876ad">precursor_tolerance</a>;</div>
<div class="line"><a name="l00158"></a><span class="lineno">  158</span>&#160;      }</div>
<div class="line"><a name="l00159"></a><span class="lineno">  159</span>&#160;</div>
<div class="line"><a name="l00160"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html#ae5fd487b73c6ee5e4a8458112bc18d06">  160</a></span>&#160;      <span class="keywordtype">bool</span> <a class="code" href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html#ae5fd487b73c6ee5e4a8458112bc18d06">operator!=</a>(<span class="keyword">const</span> <a class="code" href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html">SearchParameters</a> &amp; rhs)<span class="keyword"> const</span></div>
<div class="line"><a name="l00161"></a><span class="lineno">  161</span>&#160;<span class="keyword">      </span>{</div>
<div class="line"><a name="l00162"></a><span class="lineno">  162</span>&#160;        <span class="keywordflow">return</span> !(*<span class="keyword">this</span> == rhs);</div>
<div class="line"><a name="l00163"></a><span class="lineno">  163</span>&#160;      }</div>
<div class="line"><a name="l00164"></a><span class="lineno">  164</span>&#160;</div>
<div class="line"><a name="l00165"></a><span class="lineno">  165</span>&#160;    };</div>
<div class="line"><a name="l00166"></a><span class="lineno">  166</span>&#160;</div>
<div class="line"><a name="l00167"></a><span class="lineno">  167</span>&#160;</div>
<div class="line"><a name="l00170"></a><span class="lineno">  170</span>&#160;    <a class="code" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a>();</div>
<div class="line"><a name="l00173"></a><span class="lineno">  173</span>&#160;    <span class="keyword">virtual</span> ~<a class="code" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a>();</div>
<div class="line"><a name="l00175"></a><span class="lineno">  175</span>&#160;    <a class="code" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a> &amp; source);</div>
<div class="line"><a name="l00177"></a><span class="lineno">  177</span>&#160;    <a class="code" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a> &amp; operator=(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a> &amp; source);</div>
<div class="line"><a name="l00179"></a><span class="lineno">  179</span>&#160;    <span class="keywordtype">bool</span> operator==(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a> &amp; rhs) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00181"></a><span class="lineno">  181</span>&#160;    <span class="keywordtype">bool</span> operator!=(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a> &amp; rhs) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00183"></a><span class="lineno">  183</span>&#160;</div>
<div class="line"><a name="l00185"></a><span class="lineno">  185</span>&#160;</div>
<div class="line"><a name="l00186"></a><span class="lineno">  186</span>&#160;    <span class="keyword">const</span> std::vector&lt;ProteinHit&gt; &amp; getHits() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00189"></a><span class="lineno">  189</span>&#160;    std::vector&lt;ProteinHit&gt; &amp; getHits();</div>
<div class="line"><a name="l00191"></a><span class="lineno">  191</span>&#160;    <span class="keywordtype">void</span> insertHit(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ProteinHit.html">ProteinHit</a> &amp; input);</div>
<div class="line"><a name="l00193"></a><span class="lineno">  193</span>&#160;    <span class="keywordtype">void</span> setHits(<span class="keyword">const</span> std::vector&lt;ProteinHit&gt; &amp; hits);</div>
<div class="line"><a name="l00195"></a><span class="lineno">  195</span>&#160;    std::vector&lt;ProteinHit&gt;::iterator findHit(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; accession);</div>
<div class="line"><a name="l00196"></a><span class="lineno">  196</span>&#160;</div>
<div class="line"><a name="l00198"></a><span class="lineno">  198</span>&#160;    <span class="keyword">const</span> std::vector&lt;ProteinGroup&gt; &amp; getProteinGroups() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00200"></a><span class="lineno">  200</span>&#160;    std::vector&lt;ProteinGroup&gt; &amp; getProteinGroups();</div>
<div class="line"><a name="l00202"></a><span class="lineno">  202</span>&#160;    <span class="keywordtype">void</span> insertProteinGroup(<span class="keyword">const</span> ProteinGroup &amp; group);</div>
<div class="line"><a name="l00203"></a><span class="lineno">  203</span>&#160;</div>
<div class="line"><a name="l00205"></a><span class="lineno">  205</span>&#160;    <span class="keyword">const</span> std::vector&lt;ProteinGroup&gt; &amp; getIndistinguishableProteins() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00207"></a><span class="lineno">  207</span>&#160;    std::vector&lt;ProteinGroup&gt; &amp; getIndistinguishableProteins();</div>
<div class="line"><a name="l00209"></a><span class="lineno">  209</span>&#160;    <span class="keywordtype">void</span> insertIndistinguishableProteins(<span class="keyword">const</span> ProteinGroup &amp; group);</div>
<div class="line"><a name="l00210"></a><span class="lineno">  210</span>&#160;</div>
<div class="line"><a name="l00212"></a><span class="lineno">  212</span>&#160;    <a class="code" href="classdouble.html">DoubleReal</a> getSignificanceThreshold() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00214"></a><span class="lineno">  214</span>&#160;    <span class="keywordtype">void</span> setSignificanceThreshold(<a class="code" href="classdouble.html">DoubleReal</a> value);</div>
<div class="line"><a name="l00216"></a><span class="lineno">  216</span>&#160;    <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; getScoreType() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00218"></a><span class="lineno">  218</span>&#160;    <span class="keywordtype">void</span> setScoreType(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; type);</div>
<div class="line"><a name="l00220"></a><span class="lineno">  220</span>&#160;    <span class="keywordtype">bool</span> isHigherScoreBetter() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00222"></a><span class="lineno">  222</span>&#160;    <span class="keywordtype">void</span> setHigherScoreBetter(<span class="keywordtype">bool</span> higher_is_better);</div>
<div class="line"><a name="l00224"></a><span class="lineno">  224</span>&#160;    <span class="keywordtype">void</span> sort();</div>
<div class="line"><a name="l00226"></a><span class="lineno">  226</span>&#160;    <span class="keywordtype">void</span> assignRanks();</div>
<div class="line"><a name="l00234"></a><span class="lineno">  234</span>&#160;    <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> computeCoverage(<span class="keyword">const</span> std::vector&lt;PeptideIdentification&gt; &amp; pep_ids);</div>
<div class="line"><a name="l00236"></a><span class="lineno">  236</span>&#160;</div>
<div class="line"><a name="l00238"></a><span class="lineno">  238</span>&#160;</div>
<div class="line"><a name="l00239"></a><span class="lineno">  239</span>&#160;    <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1DateTime.html">DateTime</a> &amp; getDateTime() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00242"></a><span class="lineno">  242</span>&#160;    <span class="keywordtype">void</span> setDateTime(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1DateTime.html">DateTime</a> &amp; date);</div>
<div class="line"><a name="l00244"></a><span class="lineno">  244</span>&#160;    <span class="keywordtype">void</span> setSearchEngine(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; search_engine);</div>
<div class="line"><a name="l00246"></a><span class="lineno">  246</span>&#160;    <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; getSearchEngine() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00248"></a><span class="lineno">  248</span>&#160;    <span class="keywordtype">void</span> setSearchEngineVersion(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; search_engine_version);</div>
<div class="line"><a name="l00250"></a><span class="lineno">  250</span>&#160;    <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; getSearchEngineVersion() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00252"></a><span class="lineno">  252</span>&#160;    <span class="keywordtype">void</span> setSearchParameters(<span class="keyword">const</span> SearchParameters &amp; search_parameters);</div>
<div class="line"><a name="l00254"></a><span class="lineno">  254</span>&#160;    <span class="keyword">const</span> SearchParameters &amp; getSearchParameters() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00256"></a><span class="lineno">  256</span>&#160;    <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; getIdentifier() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00258"></a><span class="lineno">  258</span>&#160;    <span class="keywordtype">void</span> setIdentifier(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; <span class="keywordtype">id</span>);</div>
<div class="line"><a name="l00260"></a><span class="lineno">  260</span>&#160;</div>
<div class="line"><a name="l00261"></a><span class="lineno">  261</span>&#160;<span class="keyword">protected</span>:</div>
<div class="line"><a name="l00263"></a><span class="lineno">  263</span>&#160;</div>
<div class="line"><a name="l00264"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ProteinIdentification.html#ae1d43a6f8bee9f364bea98c12662e966">  264</a></span>&#160;    <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1ProteinIdentification.html#ae1d43a6f8bee9f364bea98c12662e966">id_</a>;</div>
<div class="line"><a name="l00265"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ProteinIdentification.html#a5025f2dee8f88a7632f01b5cea7043d9">  265</a></span>&#160;    <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1ProteinIdentification.html#a5025f2dee8f88a7632f01b5cea7043d9">search_engine_</a>;</div>
<div class="line"><a name="l00266"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ProteinIdentification.html#a82c64193b7343b0080e0b59d51f462b9">  266</a></span>&#160;    <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1ProteinIdentification.html#a82c64193b7343b0080e0b59d51f462b9">search_engine_version_</a>;</div>
<div class="line"><a name="l00267"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ProteinIdentification.html#a8d4d0ec9e43eeec30776ae8db269c8c8">  267</a></span>&#160;    <a class="code" href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html">SearchParameters</a> <a class="code" href="classOpenMS_1_1ProteinIdentification.html#a8d4d0ec9e43eeec30776ae8db269c8c8">search_parameters_</a>;</div>
<div class="line"><a name="l00268"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ProteinIdentification.html#ab11b7dd5f2f6ffc800af0152f5c2e69a">  268</a></span>&#160;    <a class="code" href="classOpenMS_1_1DateTime.html">DateTime</a> <a class="code" href="classOpenMS_1_1ProteinIdentification.html#ab11b7dd5f2f6ffc800af0152f5c2e69a">date_</a>;</div>
<div class="line"><a name="l00270"></a><span class="lineno">  270</span>&#160;</div>
<div class="line"><a name="l00272"></a><span class="lineno">  272</span>&#160;</div>
<div class="line"><a name="l00273"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ProteinIdentification.html#a940dace1dddca4443da1921a15603575">  273</a></span>&#160;    <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1ProteinIdentification.html#a940dace1dddca4443da1921a15603575">protein_score_type_</a>;</div>
<div class="line"><a name="l00274"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ProteinIdentification.html#a9e5d348a14e5fe639d88db39f0ff7ada">  274</a></span>&#160;    <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1ProteinIdentification.html#a9e5d348a14e5fe639d88db39f0ff7ada">higher_score_better_</a>;</div>
<div class="line"><a name="l00275"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ProteinIdentification.html#a5a059567f3e766f14ee245d880454e7c">  275</a></span>&#160;    std::vector&lt;ProteinHit&gt; <a class="code" href="classOpenMS_1_1ProteinIdentification.html#a5a059567f3e766f14ee245d880454e7c">protein_hits_</a>;</div>
<div class="line"><a name="l00276"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ProteinIdentification.html#ad8740a5936ee7eecd38542b9130f4b93">  276</a></span>&#160;    std::vector&lt;ProteinGroup&gt; <a class="code" href="classOpenMS_1_1ProteinIdentification.html#ad8740a5936ee7eecd38542b9130f4b93">protein_groups_</a>;</div>
<div class="line"><a name="l00278"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ProteinIdentification.html#ad134aae1077cd7c582d367e8fe890609">  278</a></span>&#160;    std::vector&lt;ProteinGroup&gt; <a class="code" href="classOpenMS_1_1ProteinIdentification.html#ad134aae1077cd7c582d367e8fe890609">indistinguishable_proteins_</a>;</div>
<div class="line"><a name="l00279"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ProteinIdentification.html#a47f7aa8465f37243ff2b9cca5b8cd0b4">  279</a></span>&#160;    <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1ProteinIdentification.html#a47f7aa8465f37243ff2b9cca5b8cd0b4">protein_significance_threshold_</a>;</div>
<div class="line"><a name="l00281"></a><span class="lineno">  281</span>&#160;  };</div>
<div class="line"><a name="l00282"></a><span class="lineno">  282</span>&#160;</div>
<div class="line"><a name="l00283"></a><span class="lineno">  283</span>&#160;} <span class="comment">//namespace OpenMS</span></div>
<div class="line"><a name="l00284"></a><span class="lineno">  284</span>&#160;<span class="preprocessor">#endif // OPENMS_METADATA_PROTEINIDENTIFICATION_H</span></div>
<div class="ttc" id="classOpenMS_1_1ProteinIdentification_html"><div class="ttname"><a href="classOpenMS_1_1ProteinIdentification.html">OpenMS::ProteinIdentification</a></div><div class="ttdoc">Representation of a protein identification run. </div><div class="ttdef"><b>Definition:</b> ProteinIdentification.h:61</div></div>
<div class="ttc" id="classunsigned_01int_html"><div class="ttname"><a href="classunsigned_01int.html">unsigned int</a></div></div>
<div class="ttc" id="ProteinHit_8h_html"><div class="ttname"><a href="ProteinHit_8h.html">ProteinHit.h</a></div></div>
<div class="ttc" id="structOpenMS_1_1ProteinIdentification_1_1SearchParameters_html_ae5fd487b73c6ee5e4a8458112bc18d06"><div class="ttname"><a href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html#ae5fd487b73c6ee5e4a8458112bc18d06">OpenMS::ProteinIdentification::SearchParameters::operator!=</a></div><div class="ttdeci">bool operator!=(const SearchParameters &amp;rhs) const </div><div class="ttdef"><b>Definition:</b> ProteinIdentification.h:160</div></div>
<div class="ttc" id="structOpenMS_1_1ProteinIdentification_1_1SearchParameters_html_ae525bb5a71aa3ae9d811588db4652c00"><div class="ttname"><a href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html#ae525bb5a71aa3ae9d811588db4652c00">OpenMS::ProteinIdentification::SearchParameters::db</a></div><div class="ttdeci">String db</div><div class="ttdoc">The used database. </div><div class="ttdef"><b>Definition:</b> ProteinIdentification.h:118</div></div>
<div class="ttc" id="classOpenMS_1_1String_html"><div class="ttname"><a href="classOpenMS_1_1String.html">OpenMS::String</a></div><div class="ttdoc">A more convenient string class. </div><div class="ttdef"><b>Definition:</b> String.h:56</div></div>
<div class="ttc" id="structOpenMS_1_1ProteinIdentification_1_1SearchParameters_html_afbafd06819616f82f69616ca89138c6e"><div class="ttname"><a href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html#afbafd06819616f82f69616ca89138c6e">OpenMS::ProteinIdentification::SearchParameters::operator==</a></div><div class="ttdeci">bool operator==(const SearchParameters &amp;rhs) const </div><div class="ttdef"><b>Definition:</b> ProteinIdentification.h:145</div></div>
<div class="ttc" id="structOpenMS_1_1ProteinIdentification_1_1SearchParameters_html_a490c8a0c02713ba0b9fb56164a3b6887"><div class="ttname"><a href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html#a490c8a0c02713ba0b9fb56164a3b6887">OpenMS::ProteinIdentification::SearchParameters::fixed_modifications</a></div><div class="ttdeci">std::vector&lt; String &gt; fixed_modifications</div><div class="ttdoc">Used fixed modifications. </div><div class="ttdef"><b>Definition:</b> ProteinIdentification.h:123</div></div>
<div class="ttc" id="structOpenMS_1_1ProteinIdentification_1_1SearchParameters_html_a0160159c20a3ab7cb61ce3b3091e0630"><div class="ttname"><a href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html#a0160159c20a3ab7cb61ce3b3091e0630">OpenMS::ProteinIdentification::SearchParameters::db_version</a></div><div class="ttdeci">String db_version</div><div class="ttdoc">The database version. </div><div class="ttdef"><b>Definition:</b> ProteinIdentification.h:119</div></div>
<div class="ttc" id="structOpenMS_1_1ProteinIdentification_1_1ProteinGroup_html_aaa8621a18bcb39e46cbc54376b94b66e"><div class="ttname"><a href="structOpenMS_1_1ProteinIdentification_1_1ProteinGroup.html#aaa8621a18bcb39e46cbc54376b94b66e">OpenMS::ProteinIdentification::ProteinGroup::operator==</a></div><div class="ttdeci">bool operator==(const ProteinGroup rhs) const </div><div class="ttdef"><b>Definition:</b> ProteinIdentification.h:82</div></div>
<div class="ttc" id="DateTime_8h_html"><div class="ttname"><a href="DateTime_8h.html">DateTime.h</a></div></div>
<div class="ttc" id="structOpenMS_1_1ProteinIdentification_1_1ProteinGroup_html_abb040260f33bb7404c0f2854d3a778d2"><div class="ttname"><a href="structOpenMS_1_1ProteinIdentification_1_1ProteinGroup.html#abb040260f33bb7404c0f2854d3a778d2">OpenMS::ProteinIdentification::ProteinGroup::probability</a></div><div class="ttdeci">DoubleReal probability</div><div class="ttdoc">Probability of this group. </div><div class="ttdef"><b>Definition:</b> ProteinIdentification.h:74</div></div>
<div class="ttc" id="classOpenMS_1_1ProteinIdentification_html_a5431b65220b7ad71b5e8768876ee3e53ab6f2220659ddcb84a0622d4aa4e0b112"><div class="ttname"><a href="classOpenMS_1_1ProteinIdentification.html#a5431b65220b7ad71b5e8768876ee3e53ab6f2220659ddcb84a0622d4aa4e0b112">OpenMS::ProteinIdentification::AVERAGE</a></div><div class="ttdef"><b>Definition:</b> ProteinIdentification.h:94</div></div>
<div class="ttc" id="classOpenMS_1_1ProteinIdentification_html_ac1976fd756a09ae4e26fe6b32fcb396caa87783975563314a167c39f08f065bfd"><div class="ttname"><a href="classOpenMS_1_1ProteinIdentification.html#ac1976fd756a09ae4e26fe6b32fcb396caa87783975563314a167c39f08f065bfd">OpenMS::ProteinIdentification::TRYPSIN</a></div><div class="ttdef"><b>Definition:</b> ProteinIdentification.h:103</div></div>
<div class="ttc" id="structOpenMS_1_1ProteinIdentification_1_1ProteinGroup_html_a2c5a181931200b0f5060c712f2e0568f"><div class="ttname"><a href="structOpenMS_1_1ProteinIdentification_1_1ProteinGroup.html#a2c5a181931200b0f5060c712f2e0568f">OpenMS::ProteinIdentification::ProteinGroup::ProteinGroup</a></div><div class="ttdeci">ProteinGroup()</div><div class="ttdef"><b>Definition:</b> ProteinIdentification.h:78</div></div>
<div class="ttc" id="classOpenMS_1_1ProteinIdentification_html_a82c64193b7343b0080e0b59d51f462b9"><div class="ttname"><a href="classOpenMS_1_1ProteinIdentification.html#a82c64193b7343b0080e0b59d51f462b9">OpenMS::ProteinIdentification::search_engine_version_</a></div><div class="ttdeci">String search_engine_version_</div><div class="ttdef"><b>Definition:</b> ProteinIdentification.h:266</div></div>
<div class="ttc" id="classOpenMS_1_1ProteinIdentification_html_ac1976fd756a09ae4e26fe6b32fcb396ca8013b03f6b7f2d27796adf371a715a81"><div class="ttname"><a href="classOpenMS_1_1ProteinIdentification.html#ac1976fd756a09ae4e26fe6b32fcb396ca8013b03f6b7f2d27796adf371a715a81">OpenMS::ProteinIdentification::NO_ENZYME</a></div><div class="ttdef"><b>Definition:</b> ProteinIdentification.h:107</div></div>
<div class="ttc" id="classdouble_html"><div class="ttname"><a href="classdouble.html">double</a></div></div>
<div class="ttc" id="classOpenMS_1_1ProteinIdentification_html_a81790367e26e192b9eb9c7cad5f1730d"><div class="ttname"><a href="classOpenMS_1_1ProteinIdentification.html#a81790367e26e192b9eb9c7cad5f1730d">OpenMS::ProteinIdentification::HitType</a></div><div class="ttdeci">ProteinHit HitType</div><div class="ttdoc">Hit type definition. </div><div class="ttdef"><b>Definition:</b> ProteinIdentification.h:66</div></div>
<div class="ttc" id="classOpenMS_1_1ProteinIdentification_html_ac1976fd756a09ae4e26fe6b32fcb396ca9cf5aedb487753ed0440ab34d94e1b33"><div class="ttname"><a href="classOpenMS_1_1ProteinIdentification.html#ac1976fd756a09ae4e26fe6b32fcb396ca9cf5aedb487753ed0440ab34d94e1b33">OpenMS::ProteinIdentification::PEPSIN_A</a></div><div class="ttdef"><b>Definition:</b> ProteinIdentification.h:104</div></div>
<div class="ttc" id="classOpenMS_1_1ProteinIdentification_html_ac1976fd756a09ae4e26fe6b32fcb396ca3b5e4efa6ca1ae00905ead21fe2c1e73"><div class="ttname"><a href="classOpenMS_1_1ProteinIdentification.html#ac1976fd756a09ae4e26fe6b32fcb396ca3b5e4efa6ca1ae00905ead21fe2c1e73">OpenMS::ProteinIdentification::PROTEASE_K</a></div><div class="ttdef"><b>Definition:</b> ProteinIdentification.h:105</div></div>
<div class="ttc" id="structOpenMS_1_1ProteinIdentification_1_1SearchParameters_html"><div class="ttname"><a href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html">OpenMS::ProteinIdentification::SearchParameters</a></div><div class="ttdoc">Search parameters of the DB search. </div><div class="ttdef"><b>Definition:</b> ProteinIdentification.h:115</div></div>
<div class="ttc" id="structOpenMS_1_1ProteinIdentification_1_1SearchParameters_html_a59bf6893d99c96ed73c9699b2013fb76"><div class="ttname"><a href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html#a59bf6893d99c96ed73c9699b2013fb76">OpenMS::ProteinIdentification::SearchParameters::peak_mass_tolerance</a></div><div class="ttdeci">DoubleReal peak_mass_tolerance</div><div class="ttdoc">Mass tolerance of fragment ions (Dalton) </div><div class="ttdef"><b>Definition:</b> ProteinIdentification.h:127</div></div>
<div class="ttc" id="structOpenMS_1_1ProteinIdentification_1_1SearchParameters_html_a3ebfdcd6ebd0f389bf17b098a002c531"><div class="ttname"><a href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html#a3ebfdcd6ebd0f389bf17b098a002c531">OpenMS::ProteinIdentification::SearchParameters::taxonomy</a></div><div class="ttdeci">String taxonomy</div><div class="ttdoc">The taxonomy restriction. </div><div class="ttdef"><b>Definition:</b> ProteinIdentification.h:120</div></div>
<div class="ttc" id="classOpenMS_1_1ProteinIdentification_html_a5431b65220b7ad71b5e8768876ee3e53"><div class="ttname"><a href="classOpenMS_1_1ProteinIdentification.html#a5431b65220b7ad71b5e8768876ee3e53">OpenMS::ProteinIdentification::PeakMassType</a></div><div class="ttdeci">PeakMassType</div><div class="ttdoc">Peak mass type. </div><div class="ttdef"><b>Definition:</b> ProteinIdentification.h:91</div></div>
<div class="ttc" id="structOpenMS_1_1ProteinIdentification_1_1ProteinGroup_html_a4920100bceeb1d49378a5d4370bba984"><div class="ttname"><a href="structOpenMS_1_1ProteinIdentification_1_1ProteinGroup.html#a4920100bceeb1d49378a5d4370bba984">OpenMS::ProteinIdentification::ProteinGroup::accessions</a></div><div class="ttdeci">StringList accessions</div><div class="ttdoc">Accessions of (indistinguishable) proteins that belong to the same group. </div><div class="ttdef"><b>Definition:</b> ProteinIdentification.h:76</div></div>
<div class="ttc" id="classOpenMS_1_1ProteinIdentification_html_ac1976fd756a09ae4e26fe6b32fcb396c"><div class="ttname"><a href="classOpenMS_1_1ProteinIdentification.html#ac1976fd756a09ae4e26fe6b32fcb396c">OpenMS::ProteinIdentification::DigestionEnzyme</a></div><div class="ttdeci">DigestionEnzyme</div><div class="ttdef"><b>Definition:</b> ProteinIdentification.h:101</div></div>
<div class="ttc" id="classOpenMS_1_1ProteinIdentification_html_a5a059567f3e766f14ee245d880454e7c"><div class="ttname"><a href="classOpenMS_1_1ProteinIdentification.html#a5a059567f3e766f14ee245d880454e7c">OpenMS::ProteinIdentification::protein_hits_</a></div><div class="ttdeci">std::vector&lt; ProteinHit &gt; protein_hits_</div><div class="ttdef"><b>Definition:</b> ProteinIdentification.h:275</div></div>
<div class="ttc" id="classOpenMS_1_1ProteinIdentification_html_a47f7aa8465f37243ff2b9cca5b8cd0b4"><div class="ttname"><a href="classOpenMS_1_1ProteinIdentification.html#a47f7aa8465f37243ff2b9cca5b8cd0b4">OpenMS::ProteinIdentification::protein_significance_threshold_</a></div><div class="ttdeci">DoubleReal protein_significance_threshold_</div><div class="ttdef"><b>Definition:</b> ProteinIdentification.h:279</div></div>
<div class="ttc" id="classOpenMS_1_1ProteinIdentification_html_a940dace1dddca4443da1921a15603575"><div class="ttname"><a href="classOpenMS_1_1ProteinIdentification.html#a940dace1dddca4443da1921a15603575">OpenMS::ProteinIdentification::protein_score_type_</a></div><div class="ttdeci">String protein_score_type_</div><div class="ttdef"><b>Definition:</b> ProteinIdentification.h:273</div></div>
<div class="ttc" id="structOpenMS_1_1ProteinIdentification_1_1SearchParameters_html_a9665390243976d08d254b1d2e83876ad"><div class="ttname"><a href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html#a9665390243976d08d254b1d2e83876ad">OpenMS::ProteinIdentification::SearchParameters::precursor_tolerance</a></div><div class="ttdeci">DoubleReal precursor_tolerance</div><div class="ttdoc">Mass tolerance of precursor ions (Dalton) </div><div class="ttdef"><b>Definition:</b> ProteinIdentification.h:128</div></div>
<div class="ttc" id="classOpenMS_1_1ProteinIdentification_html_ae1d43a6f8bee9f364bea98c12662e966"><div class="ttname"><a href="classOpenMS_1_1ProteinIdentification.html#ae1d43a6f8bee9f364bea98c12662e966">OpenMS::ProteinIdentification::id_</a></div><div class="ttdeci">String id_</div><div class="ttdef"><b>Definition:</b> ProteinIdentification.h:264</div></div>
<div class="ttc" id="MetaInfoInterface_8h_html"><div class="ttname"><a href="MetaInfoInterface_8h.html">MetaInfoInterface.h</a></div></div>
<div class="ttc" id="structOpenMS_1_1ProteinIdentification_1_1SearchParameters_html_af70dd1b4c626832e04f0cc7fb04ac0e2"><div class="ttname"><a href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html#af70dd1b4c626832e04f0cc7fb04ac0e2">OpenMS::ProteinIdentification::SearchParameters::missed_cleavages</a></div><div class="ttdeci">UInt missed_cleavages</div><div class="ttdoc">The number of allowed missed cleavages. </div><div class="ttdef"><b>Definition:</b> ProteinIdentification.h:126</div></div>
<div class="ttc" id="classOpenMS_1_1MetaInfoInterface_html"><div class="ttname"><a href="classOpenMS_1_1MetaInfoInterface.html">OpenMS::MetaInfoInterface</a></div><div class="ttdoc">Interface for classes that can store arbitrary meta information (Type-Name-Value tuples). </div><div class="ttdef"><b>Definition:</b> MetaInfoInterface.h:61</div></div>
<div class="ttc" id="classOpenMS_1_1ProteinIdentification_html_ad8740a5936ee7eecd38542b9130f4b93"><div class="ttname"><a href="classOpenMS_1_1ProteinIdentification.html#ad8740a5936ee7eecd38542b9130f4b93">OpenMS::ProteinIdentification::protein_groups_</a></div><div class="ttdeci">std::vector&lt; ProteinGroup &gt; protein_groups_</div><div class="ttdef"><b>Definition:</b> ProteinIdentification.h:276</div></div>
<div class="ttc" id="classOpenMS_1_1ProteinIdentification_html_a5025f2dee8f88a7632f01b5cea7043d9"><div class="ttname"><a href="classOpenMS_1_1ProteinIdentification.html#a5025f2dee8f88a7632f01b5cea7043d9">OpenMS::ProteinIdentification::search_engine_</a></div><div class="ttdeci">String search_engine_</div><div class="ttdef"><b>Definition:</b> ProteinIdentification.h:265</div></div>
<div class="ttc" id="classOpenMS_1_1ProteinIdentification_html_ac1976fd756a09ae4e26fe6b32fcb396ca36a56e667bdbe75daa08c655e85ec49a"><div class="ttname"><a href="classOpenMS_1_1ProteinIdentification.html#ac1976fd756a09ae4e26fe6b32fcb396ca36a56e667bdbe75daa08c655e85ec49a">OpenMS::ProteinIdentification::UNKNOWN_ENZYME</a></div><div class="ttdef"><b>Definition:</b> ProteinIdentification.h:108</div></div>
<div class="ttc" id="classOpenMS_1_1ProteinHit_html"><div class="ttname"><a href="classOpenMS_1_1ProteinHit.html">OpenMS::ProteinHit</a></div><div class="ttdoc">Representation of a protein hit. </div><div class="ttdef"><b>Definition:</b> ProteinHit.h:54</div></div>
<div class="ttc" id="classOpenMS_1_1ProteinIdentification_html_a9e5d348a14e5fe639d88db39f0ff7ada"><div class="ttname"><a href="classOpenMS_1_1ProteinIdentification.html#a9e5d348a14e5fe639d88db39f0ff7ada">OpenMS::ProteinIdentification::higher_score_better_</a></div><div class="ttdeci">bool higher_score_better_</div><div class="ttdef"><b>Definition:</b> ProteinIdentification.h:274</div></div>
<div class="ttc" id="classOpenMS_1_1ProteinIdentification_html_ab11b7dd5f2f6ffc800af0152f5c2e69a"><div class="ttname"><a href="classOpenMS_1_1ProteinIdentification.html#ab11b7dd5f2f6ffc800af0152f5c2e69a">OpenMS::ProteinIdentification::date_</a></div><div class="ttdeci">DateTime date_</div><div class="ttdef"><b>Definition:</b> ProteinIdentification.h:268</div></div>
<div class="ttc" id="classOpenMS_1_1ProteinIdentification_html_ac1976fd756a09ae4e26fe6b32fcb396ca240cc037883891d0eb859a89530893ba"><div class="ttname"><a href="classOpenMS_1_1ProteinIdentification.html#ac1976fd756a09ae4e26fe6b32fcb396ca240cc037883891d0eb859a89530893ba">OpenMS::ProteinIdentification::CHYMOTRYPSIN</a></div><div class="ttdef"><b>Definition:</b> ProteinIdentification.h:106</div></div>
<div class="ttc" id="classOpenMS_1_1ProteinIdentification_html_a5431b65220b7ad71b5e8768876ee3e53aba27416c974c26497ea0f4aa59fcf669"><div class="ttname"><a href="classOpenMS_1_1ProteinIdentification.html#a5431b65220b7ad71b5e8768876ee3e53aba27416c974c26497ea0f4aa59fcf669">OpenMS::ProteinIdentification::MONOISOTOPIC</a></div><div class="ttdef"><b>Definition:</b> ProteinIdentification.h:93</div></div>
<div class="ttc" id="classOpenMS_1_1StringList_html"><div class="ttname"><a href="classOpenMS_1_1StringList.html">OpenMS::StringList</a></div><div class="ttdoc">String list. </div><div class="ttdef"><b>Definition:</b> StringList.h:56</div></div>
<div class="ttc" id="group__Concept_html_gaf9ecec2d692138fab9167164a457cbd4"><div class="ttname"><a href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">OpenMS::Size</a></div><div class="ttdeci">size_t Size</div><div class="ttdoc">Size type e.g. used as variable which can hold result of size() </div><div class="ttdef"><b>Definition:</b> Types.h:144</div></div>
<div class="ttc" id="classOpenMS_1_1DateTime_html"><div class="ttname"><a href="classOpenMS_1_1DateTime.html">OpenMS::DateTime</a></div><div class="ttdoc">DateTime Class. </div><div class="ttdef"><b>Definition:</b> DateTime.h:55</div></div>
<div class="ttc" id="classOpenMS_1_1ProteinIdentification_html_ad134aae1077cd7c582d367e8fe890609"><div class="ttname"><a href="classOpenMS_1_1ProteinIdentification.html#ad134aae1077cd7c582d367e8fe890609">OpenMS::ProteinIdentification::indistinguishable_proteins_</a></div><div class="ttdeci">std::vector&lt; ProteinGroup &gt; indistinguishable_proteins_</div><div class="ttdoc">Indistinguishable proteins: accessions[0] is &amp;quot;group leader&amp;quot;, probability is meaningless. </div><div class="ttdef"><b>Definition:</b> ProteinIdentification.h:278</div></div>
<div class="ttc" id="structOpenMS_1_1ProteinIdentification_1_1SearchParameters_html_a99f4b7d19585e6f1251cc9d8e1367f77"><div class="ttname"><a href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html#a99f4b7d19585e6f1251cc9d8e1367f77">OpenMS::ProteinIdentification::SearchParameters::SearchParameters</a></div><div class="ttdeci">SearchParameters()</div><div class="ttdef"><b>Definition:</b> ProteinIdentification.h:130</div></div>
<div class="ttc" id="structOpenMS_1_1ProteinIdentification_1_1SearchParameters_html_aef9bb017f25e4697cca5e2793f91b267"><div class="ttname"><a href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html#aef9bb017f25e4697cca5e2793f91b267">OpenMS::ProteinIdentification::SearchParameters::enzyme</a></div><div class="ttdeci">DigestionEnzyme enzyme</div><div class="ttdoc">The enzyme used for cleavage. </div><div class="ttdef"><b>Definition:</b> ProteinIdentification.h:125</div></div>
<div class="ttc" id="structOpenMS_1_1ProteinIdentification_1_1SearchParameters_html_ae19806728daee03d5fc75855db1152d4"><div class="ttname"><a href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html#ae19806728daee03d5fc75855db1152d4">OpenMS::ProteinIdentification::SearchParameters::mass_type</a></div><div class="ttdeci">PeakMassType mass_type</div><div class="ttdoc">Mass type of the peaks. </div><div class="ttdef"><b>Definition:</b> ProteinIdentification.h:122</div></div>
<div class="ttc" id="classOpenMS_1_1ProteinIdentification_html_a8d4d0ec9e43eeec30776ae8db269c8c8"><div class="ttname"><a href="classOpenMS_1_1ProteinIdentification.html#a8d4d0ec9e43eeec30776ae8db269c8c8">OpenMS::ProteinIdentification::search_parameters_</a></div><div class="ttdeci">SearchParameters search_parameters_</div><div class="ttdef"><b>Definition:</b> ProteinIdentification.h:267</div></div>
<div class="ttc" id="structOpenMS_1_1ProteinIdentification_1_1SearchParameters_html_a6b3f6ef19caf97c201fba99444bf0663"><div class="ttname"><a href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html#a6b3f6ef19caf97c201fba99444bf0663">OpenMS::ProteinIdentification::SearchParameters::charges</a></div><div class="ttdeci">String charges</div><div class="ttdoc">The allowed charges for the search. </div><div class="ttdef"><b>Definition:</b> ProteinIdentification.h:121</div></div>
<div class="ttc" id="structOpenMS_1_1ProteinIdentification_1_1ProteinGroup_html"><div class="ttname"><a href="structOpenMS_1_1ProteinIdentification_1_1ProteinGroup.html">OpenMS::ProteinIdentification::ProteinGroup</a></div><div class="ttdoc">Bundles multiple (e.g. indistinguishable) proteins in a group. </div><div class="ttdef"><b>Definition:</b> ProteinIdentification.h:71</div></div>
<div class="ttc" id="structOpenMS_1_1ProteinIdentification_1_1SearchParameters_html_adeefbd81d0184c04768844df11e5b979"><div class="ttname"><a href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html#adeefbd81d0184c04768844df11e5b979">OpenMS::ProteinIdentification::SearchParameters::variable_modifications</a></div><div class="ttdeci">std::vector&lt; String &gt; variable_modifications</div><div class="ttdoc">Allowed variable modifications. </div><div class="ttdef"><b>Definition:</b> ProteinIdentification.h:124</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 11:19:19 using doxygen 1.8.5</font></TD>
</TR>
</TABLE>
</BODY>
</HTML>