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
|
<HTML>
<HEAD>
<TITLE>ConsensusXMLFile.h Source File</TITLE>
<LINK HREF="doxygen.css" REL="stylesheet" TYPE="text/css">
<LINK HREF="style_ini.css" REL="stylesheet" TYPE="text/css">
</HEAD>
<BODY BGCOLOR="#FFFFFF">
<A href="index.html">Home</A> ·
<A href="classes.html">Classes</A> ·
<A href="annotated.html">Annotated Classes</A> ·
<A href="modules.html">Modules</A> ·
<A href="functions_func.html">Members</A> ·
<A href="namespaces.html">Namespaces</A> ·
<A href="pages.html">Related Pages</A>
<HR style="height:1px; border:none; border-top:1px solid #c0c0c0;">
<!-- Generated by Doxygen 1.8.5 -->
<div id="nav-path" class="navpath">
<ul>
<li class="navelem"><a class="el" href="dir_e770f0cf77e550adde3f44739ef529fe.html">include</a></li><li class="navelem"><a class="el" href="dir_6a63c4937d4da007e55fff5dcf71e0f8.html">OpenMS</a></li><li class="navelem"><a class="el" href="dir_d1695c75ee0aa48d87e52f45c7decd7a.html">FORMAT</a></li> </ul>
</div>
</div><!-- top -->
<div class="header">
<div class="headertitle">
<div class="title">ConsensusXMLFile.h</div> </div>
</div><!--header-->
<div class="contents">
<a href="ConsensusXMLFile_8h.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="comment">// OpenMS -- Open-Source Mass Spectrometry</span></div>
<div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="comment">// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,</span></div>
<div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="comment">// ETH Zurich, and Freie Universitaet Berlin 2002-2013.</span></div>
<div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="comment">//</span></div>
<div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="comment">// This software is released under a three-clause BSD license:</span></div>
<div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="comment">// * Redistributions of source code must retain the above copyright</span></div>
<div class="line"><a name="l00009"></a><span class="lineno"> 9</span> <span class="comment">// notice, this list of conditions and the following disclaimer.</span></div>
<div class="line"><a name="l00010"></a><span class="lineno"> 10</span> <span class="comment">// * Redistributions in binary form must reproduce the above copyright</span></div>
<div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="comment">// notice, this list of conditions and the following disclaimer in the</span></div>
<div class="line"><a name="l00012"></a><span class="lineno"> 12</span> <span class="comment">// documentation and/or other materials provided with the distribution.</span></div>
<div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="comment">// * Neither the name of any author or any participating institution</span></div>
<div class="line"><a name="l00014"></a><span class="lineno"> 14</span> <span class="comment">// may be used to endorse or promote products derived from this software</span></div>
<div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="comment">// without specific prior written permission.</span></div>
<div class="line"><a name="l00016"></a><span class="lineno"> 16</span> <span class="comment">// For a full list of authors, refer to the file AUTHORS.</span></div>
<div class="line"><a name="l00017"></a><span class="lineno"> 17</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00018"></a><span class="lineno"> 18</span> <span class="comment">// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"</span></div>
<div class="line"><a name="l00019"></a><span class="lineno"> 19</span> <span class="comment">// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE</span></div>
<div class="line"><a name="l00020"></a><span class="lineno"> 20</span> <span class="comment">// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE</span></div>
<div class="line"><a name="l00021"></a><span class="lineno"> 21</span> <span class="comment">// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING</span></div>
<div class="line"><a name="l00022"></a><span class="lineno"> 22</span> <span class="comment">// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,</span></div>
<div class="line"><a name="l00023"></a><span class="lineno"> 23</span> <span class="comment">// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,</span></div>
<div class="line"><a name="l00024"></a><span class="lineno"> 24</span> <span class="comment">// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;</span></div>
<div class="line"><a name="l00025"></a><span class="lineno"> 25</span> <span class="comment">// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,</span></div>
<div class="line"><a name="l00026"></a><span class="lineno"> 26</span> <span class="comment">// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR</span></div>
<div class="line"><a name="l00027"></a><span class="lineno"> 27</span> <span class="comment">// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF</span></div>
<div class="line"><a name="l00028"></a><span class="lineno"> 28</span> <span class="comment">// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</span></div>
<div class="line"><a name="l00029"></a><span class="lineno"> 29</span> <span class="comment">//</span></div>
<div class="line"><a name="l00030"></a><span class="lineno"> 30</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00031"></a><span class="lineno"> 31</span> <span class="comment">// $Maintainer: Clemens Groepl $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno"> 32</span> <span class="comment">// $Authors: Clemens Groepl, Marc Sturm $</span></div>
<div class="line"><a name="l00033"></a><span class="lineno"> 33</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00034"></a><span class="lineno"> 34</span> </div>
<div class="line"><a name="l00035"></a><span class="lineno"> 35</span> <span class="preprocessor">#ifndef OPENMS_FORMAT_CONSENSUSXMLFILE_H</span></div>
<div class="line"><a name="l00036"></a><span class="lineno"> 36</span> <span class="preprocessor"></span><span class="preprocessor">#define OPENMS_FORMAT_CONSENSUSXMLFILE_H</span></div>
<div class="line"><a name="l00037"></a><span class="lineno"> 37</span> <span class="preprocessor"></span></div>
<div class="line"><a name="l00038"></a><span class="lineno"> 38</span> <span class="preprocessor">#include <<a class="code" href="ProgressLogger_8h.html">OpenMS/CONCEPT/ProgressLogger.h</a>></span></div>
<div class="line"><a name="l00039"></a><span class="lineno"> 39</span> <span class="preprocessor">#include <<a class="code" href="XMLHandler_8h.html">OpenMS/FORMAT/HANDLERS/XMLHandler.h</a>></span></div>
<div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="preprocessor">#include <<a class="code" href="PeakFileOptions_8h.html">OpenMS/FORMAT/OPTIONS/PeakFileOptions.h</a>></span></div>
<div class="line"><a name="l00041"></a><span class="lineno"> 41</span> <span class="preprocessor">#include <<a class="code" href="XMLFile_8h.html">OpenMS/FORMAT/XMLFile.h</a>></span></div>
<div class="line"><a name="l00042"></a><span class="lineno"> 42</span> <span class="preprocessor">#include <<a class="code" href="ConsensusMap_8h.html">OpenMS/KERNEL/ConsensusMap.h</a>></span></div>
<div class="line"><a name="l00043"></a><span class="lineno"> 43</span> </div>
<div class="line"><a name="l00044"></a><span class="lineno"> 44</span> <span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00045"></a><span class="lineno"> 45</span> {</div>
<div class="line"><a name="l00059"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ConsensusXMLFile.html"> 59</a></span>  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1ConsensusXMLFile.html">ConsensusXMLFile</a> :</div>
<div class="line"><a name="l00060"></a><span class="lineno"> 60</span>  <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1Internal_1_1XMLHandler.html">Internal::XMLHandler</a>,</div>
<div class="line"><a name="l00061"></a><span class="lineno"> 61</span>  <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1Internal_1_1XMLFile.html">Internal::XMLFile</a>,</div>
<div class="line"><a name="l00062"></a><span class="lineno"> 62</span>  <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a></div>
<div class="line"><a name="l00063"></a><span class="lineno"> 63</span>  {</div>
<div class="line"><a name="l00064"></a><span class="lineno"> 64</span> <span class="keyword">public</span>:</div>
<div class="line"><a name="l00066"></a><span class="lineno"> 66</span>  <a class="code" href="classOpenMS_1_1ConsensusXMLFile.html">ConsensusXMLFile</a>();</div>
<div class="line"><a name="l00068"></a><span class="lineno"> 68</span>  ~<a class="code" href="classOpenMS_1_1ConsensusXMLFile.html">ConsensusXMLFile</a>();</div>
<div class="line"><a name="l00069"></a><span class="lineno"> 69</span> </div>
<div class="line"><a name="l00070"></a><span class="lineno"> 70</span> </div>
<div class="line"><a name="l00078"></a><span class="lineno"> 78</span>  <span class="keywordtype">void</span> load(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & filename, <a class="code" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a> & map);</div>
<div class="line"><a name="l00079"></a><span class="lineno"> 79</span> </div>
<div class="line"><a name="l00087"></a><span class="lineno"> 87</span>  <span class="keywordtype">void</span> store(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & filename, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a> & consensus_map);</div>
<div class="line"><a name="l00088"></a><span class="lineno"> 88</span> </div>
<div class="line"><a name="l00090"></a><span class="lineno"> 90</span>  <a class="code" href="classOpenMS_1_1PeakFileOptions.html">PeakFileOptions</a> & getOptions();</div>
<div class="line"><a name="l00091"></a><span class="lineno"> 91</span> </div>
<div class="line"><a name="l00093"></a><span class="lineno"> 93</span>  <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1PeakFileOptions.html">PeakFileOptions</a> & getOptions() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00094"></a><span class="lineno"> 94</span> </div>
<div class="line"><a name="l00095"></a><span class="lineno"> 95</span> <span class="keyword">protected</span>:</div>
<div class="line"><a name="l00096"></a><span class="lineno"> 96</span> </div>
<div class="line"><a name="l00097"></a><span class="lineno"> 97</span>  <span class="comment">// Docu in base class</span></div>
<div class="line"><a name="l00098"></a><span class="lineno"> 98</span>  <span class="keyword">virtual</span> <span class="keywordtype">void</span> endElement(<span class="keyword">const</span> XMLCh * <span class="keyword">const</span> <span class="comment">/*uri*/</span>, <span class="keyword">const</span> XMLCh * <span class="keyword">const</span> <span class="comment">/*local_name*/</span>, <span class="keyword">const</span> XMLCh * <span class="keyword">const</span> qname);</div>
<div class="line"><a name="l00099"></a><span class="lineno"> 99</span> </div>
<div class="line"><a name="l00100"></a><span class="lineno"> 100</span>  <span class="comment">// Docu in base class</span></div>
<div class="line"><a name="l00101"></a><span class="lineno"> 101</span>  <span class="keyword">virtual</span> <span class="keywordtype">void</span> startElement(<span class="keyword">const</span> XMLCh * <span class="keyword">const</span> <span class="comment">/*uri*/</span>, <span class="keyword">const</span> XMLCh * <span class="keyword">const</span> <span class="comment">/*local_name*/</span>, <span class="keyword">const</span> XMLCh * <span class="keyword">const</span> qname, <span class="keyword">const</span> xercesc::Attributes & attributes);</div>
<div class="line"><a name="l00102"></a><span class="lineno"> 102</span> </div>
<div class="line"><a name="l00103"></a><span class="lineno"> 103</span>  <span class="comment">// Docu in base class</span></div>
<div class="line"><a name="l00104"></a><span class="lineno"> 104</span>  <span class="keyword">virtual</span> <span class="keywordtype">void</span> characters(<span class="keyword">const</span> XMLCh * <span class="keyword">const</span> chars, <span class="keyword">const</span> XMLSize_t length);</div>
<div class="line"><a name="l00105"></a><span class="lineno"> 105</span> </div>
<div class="line"><a name="l00106"></a><span class="lineno"> 106</span> </div>
<div class="line"><a name="l00108"></a><span class="lineno"> 108</span>  <span class="keywordtype">void</span> writePeptideIdentification_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & filename, std::ostream & os, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> & <span class="keywordtype">id</span>, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & tag_name, <a class="code" href="classunsigned_01int.html">UInt</a> indentation_level);</div>
<div class="line"><a name="l00109"></a><span class="lineno"> 109</span> </div>
<div class="line"><a name="l00110"></a><span class="lineno"> 110</span> </div>
<div class="line"><a name="l00112"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ConsensusXMLFile.html#a654a0b5941d937e303c64bc9e732baec"> 112</a></span>  <a class="code" href="classOpenMS_1_1PeakFileOptions.html">PeakFileOptions</a> <a class="code" href="classOpenMS_1_1ConsensusXMLFile.html#a654a0b5941d937e303c64bc9e732baec">options_</a>;</div>
<div class="line"><a name="l00113"></a><span class="lineno"> 113</span> </div>
<div class="line"><a name="l00115"></a><span class="lineno"> 115</span> </div>
<div class="line"><a name="l00116"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ConsensusXMLFile.html#a98696316ca504aafbaa7eb2f2c062df6"> 116</a></span>  <a class="code" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a> * <a class="code" href="classOpenMS_1_1ConsensusXMLFile.html#a98696316ca504aafbaa7eb2f2c062df6">consensus_map_</a>;</div>
<div class="line"><a name="l00117"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ConsensusXMLFile.html#a65b28df44922cbdc28bcc48bf71afc66"> 117</a></span>  <a class="code" href="classOpenMS_1_1ConsensusFeature.html">ConsensusFeature</a> <a class="code" href="classOpenMS_1_1ConsensusXMLFile.html#a65b28df44922cbdc28bcc48bf71afc66">act_cons_element_</a>;</div>
<div class="line"><a name="l00118"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ConsensusXMLFile.html#a590ed25661a837bfedb38402e2c50b47"> 118</a></span>  <a class="code" href="classOpenMS_1_1DPosition.html">DPosition<2></a> <a class="code" href="classOpenMS_1_1ConsensusXMLFile.html#a590ed25661a837bfedb38402e2c50b47">pos_</a>;</div>
<div class="line"><a name="l00119"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ConsensusXMLFile.html#a05fe9910cacd8b17b3c6ac120135a6fc"> 119</a></span>  <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1ConsensusXMLFile.html#a05fe9910cacd8b17b3c6ac120135a6fc">it_</a>;</div>
<div class="line"><a name="l00121"></a><span class="lineno"> 121</span> </div>
<div class="line"><a name="l00123"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ConsensusXMLFile.html#a23a7355f9a0e61f3990a763f0fa7c528"> 123</a></span>  <a class="code" href="classOpenMS_1_1MetaInfoInterface.html">MetaInfoInterface</a> * <a class="code" href="classOpenMS_1_1ConsensusXMLFile.html#a23a7355f9a0e61f3990a763f0fa7c528">last_meta_</a>;</div>
<div class="line"><a name="l00125"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ConsensusXMLFile.html#a5e548fc9726de1f64e315fa215f4de19"> 125</a></span>  <a class="code" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a> <a class="code" href="classOpenMS_1_1ConsensusXMLFile.html#a5e548fc9726de1f64e315fa215f4de19">prot_id_</a>;</div>
<div class="line"><a name="l00127"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ConsensusXMLFile.html#ab59916b51e0840799c0a78ed04d7f859"> 127</a></span>  <a class="code" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> <a class="code" href="classOpenMS_1_1ConsensusXMLFile.html#ab59916b51e0840799c0a78ed04d7f859">pep_id_</a>;</div>
<div class="line"><a name="l00129"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ConsensusXMLFile.html#a855d1cd159f5a8295c3d6be4327a1542"> 129</a></span>  <a class="code" href="classOpenMS_1_1ProteinHit.html">ProteinHit</a> <a class="code" href="classOpenMS_1_1ConsensusXMLFile.html#a855d1cd159f5a8295c3d6be4327a1542">prot_hit_</a>;</div>
<div class="line"><a name="l00131"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ConsensusXMLFile.html#a963bc7db375d58bd099601271cc7a011"> 131</a></span>  <a class="code" href="classOpenMS_1_1PeptideHit.html">PeptideHit</a> <a class="code" href="classOpenMS_1_1ConsensusXMLFile.html#a963bc7db375d58bd099601271cc7a011">pep_hit_</a>;</div>
<div class="line"><a name="l00133"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ConsensusXMLFile.html#ad23fa42c762a035786d56a07e2f1ea16"> 133</a></span>  <a class="code" href="classOpenMS_1_1Map.html">Map<String, String></a> <a class="code" href="classOpenMS_1_1ConsensusXMLFile.html#ad23fa42c762a035786d56a07e2f1ea16">proteinid_to_accession_</a>;</div>
<div class="line"><a name="l00135"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ConsensusXMLFile.html#a15e5e3bc144b437972738bf1d168b741"> 135</a></span>  <a class="code" href="classOpenMS_1_1Map.html">Map<String, Size></a> <a class="code" href="classOpenMS_1_1ConsensusXMLFile.html#a15e5e3bc144b437972738bf1d168b741">accession_to_id_</a>;</div>
<div class="line"><a name="l00137"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ConsensusXMLFile.html#a65fe117944045e89e6add20e3f7ba912"> 137</a></span>  <a class="code" href="classOpenMS_1_1Map.html">Map<String, String></a> <a class="code" href="classOpenMS_1_1ConsensusXMLFile.html#a65fe117944045e89e6add20e3f7ba912">identifier_id_</a>;</div>
<div class="line"><a name="l00139"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ConsensusXMLFile.html#a3b0075b28e6591f39fafa2720002c5d6"> 139</a></span>  <a class="code" href="classOpenMS_1_1Map.html">Map<String, String></a> <a class="code" href="classOpenMS_1_1ConsensusXMLFile.html#a3b0075b28e6591f39fafa2720002c5d6">id_identifier_</a>;</div>
<div class="line"><a name="l00141"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ConsensusXMLFile.html#a22cfe808d1f3b2c6b9f97ccde38e6ec4"> 141</a></span>  <a class="code" href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html">ProteinIdentification::SearchParameters</a> <a class="code" href="classOpenMS_1_1ConsensusXMLFile.html#a22cfe808d1f3b2c6b9f97ccde38e6ec4">search_param_</a>;</div>
<div class="line"><a name="l00142"></a><span class="lineno"> 142</span> </div>
<div class="line"><a name="l00143"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ConsensusXMLFile.html#a8e17f7a3517f0ea0f31fd4c9d7608e3c"> 143</a></span>  <a class="code" href="classunsigned_01int.html">UInt</a> <a class="code" href="classOpenMS_1_1ConsensusXMLFile.html#a8e17f7a3517f0ea0f31fd4c9d7608e3c">progress_</a>;</div>
<div class="line"><a name="l00144"></a><span class="lineno"> 144</span> </div>
<div class="line"><a name="l00145"></a><span class="lineno"> 145</span>  };</div>
<div class="line"><a name="l00146"></a><span class="lineno"> 146</span> } <span class="comment">// namespace OpenMS</span></div>
<div class="line"><a name="l00147"></a><span class="lineno"> 147</span> </div>
<div class="line"><a name="l00148"></a><span class="lineno"> 148</span> <span class="preprocessor">#endif // OPENMS_FOMAT_CONSENSUSXMLFILE_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="PeakFileOptions_8h_html"><div class="ttname"><a href="PeakFileOptions_8h.html">PeakFileOptions.h</a></div></div>
<div class="ttc" id="classunsigned_01int_html"><div class="ttname"><a href="classunsigned_01int.html">unsigned int</a></div></div>
<div class="ttc" id="classOpenMS_1_1ConsensusXMLFile_html_a98696316ca504aafbaa7eb2f2c062df6"><div class="ttname"><a href="classOpenMS_1_1ConsensusXMLFile.html#a98696316ca504aafbaa7eb2f2c062df6">OpenMS::ConsensusXMLFile::consensus_map_</a></div><div class="ttdeci">ConsensusMap * consensus_map_</div><div class="ttdef"><b>Definition:</b> ConsensusXMLFile.h:116</div></div>
<div class="ttc" id="classOpenMS_1_1String_html"><div class="ttname"><a href="classOpenMS_1_1String.html">OpenMS::String</a></div><div class="ttdoc">A more convenient string class. </div><div class="ttdef"><b>Definition:</b> String.h:56</div></div>
<div class="ttc" id="classOpenMS_1_1ConsensusXMLFile_html_a3b0075b28e6591f39fafa2720002c5d6"><div class="ttname"><a href="classOpenMS_1_1ConsensusXMLFile.html#a3b0075b28e6591f39fafa2720002c5d6">OpenMS::ConsensusXMLFile::id_identifier_</a></div><div class="ttdeci">Map< String, String > id_identifier_</div><div class="ttdoc">Map from file xs:id to identification run identifier (for linking peptide identifications to the corr...</div><div class="ttdef"><b>Definition:</b> ConsensusXMLFile.h:139</div></div>
<div class="ttc" id="classOpenMS_1_1ConsensusXMLFile_html_a654a0b5941d937e303c64bc9e732baec"><div class="ttname"><a href="classOpenMS_1_1ConsensusXMLFile.html#a654a0b5941d937e303c64bc9e732baec">OpenMS::ConsensusXMLFile::options_</a></div><div class="ttdeci">PeakFileOptions options_</div><div class="ttdoc">Options that can be set. </div><div class="ttdef"><b>Definition:</b> ConsensusXMLFile.h:112</div></div>
<div class="ttc" id="ConsensusMap_8h_html"><div class="ttname"><a href="ConsensusMap_8h.html">ConsensusMap.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1ConsensusXMLFile_html_a22cfe808d1f3b2c6b9f97ccde38e6ec4"><div class="ttname"><a href="classOpenMS_1_1ConsensusXMLFile.html#a22cfe808d1f3b2c6b9f97ccde38e6ec4">OpenMS::ConsensusXMLFile::search_param_</a></div><div class="ttdeci">ProteinIdentification::SearchParameters search_param_</div><div class="ttdoc">Temporary search parameters file. </div><div class="ttdef"><b>Definition:</b> ConsensusXMLFile.h:141</div></div>
<div class="ttc" id="classOpenMS_1_1ConsensusXMLFile_html_a65b28df44922cbdc28bcc48bf71afc66"><div class="ttname"><a href="classOpenMS_1_1ConsensusXMLFile.html#a65b28df44922cbdc28bcc48bf71afc66">OpenMS::ConsensusXMLFile::act_cons_element_</a></div><div class="ttdeci">ConsensusFeature act_cons_element_</div><div class="ttdef"><b>Definition:</b> ConsensusXMLFile.h:117</div></div>
<div class="ttc" id="ProgressLogger_8h_html"><div class="ttname"><a href="ProgressLogger_8h.html">ProgressLogger.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1ConsensusXMLFile_html_a855d1cd159f5a8295c3d6be4327a1542"><div class="ttname"><a href="classOpenMS_1_1ConsensusXMLFile.html#a855d1cd159f5a8295c3d6be4327a1542">OpenMS::ConsensusXMLFile::prot_hit_</a></div><div class="ttdeci">ProteinHit prot_hit_</div><div class="ttdoc">Temporary protein hit. </div><div class="ttdef"><b>Definition:</b> ConsensusXMLFile.h:129</div></div>
<div class="ttc" id="classOpenMS_1_1ConsensusXMLFile_html_a5e548fc9726de1f64e315fa215f4de19"><div class="ttname"><a href="classOpenMS_1_1ConsensusXMLFile.html#a5e548fc9726de1f64e315fa215f4de19">OpenMS::ConsensusXMLFile::prot_id_</a></div><div class="ttdeci">ProteinIdentification prot_id_</div><div class="ttdoc">Temporary protein ProteinIdentification. </div><div class="ttdef"><b>Definition:</b> ConsensusXMLFile.h:125</div></div>
<div class="ttc" id="classOpenMS_1_1ConsensusMap_html"><div class="ttname"><a href="classOpenMS_1_1ConsensusMap.html">OpenMS::ConsensusMap</a></div><div class="ttdoc">A container for consensus elements. </div><div class="ttdef"><b>Definition:</b> ConsensusMap.h:60</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1XMLHandler_html"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1XMLHandler.html">OpenMS::Internal::XMLHandler</a></div><div class="ttdoc">Base class for XML handlers. </div><div class="ttdef"><b>Definition:</b> XMLHandler.h:89</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_1ConsensusXMLFile_html_a963bc7db375d58bd099601271cc7a011"><div class="ttname"><a href="classOpenMS_1_1ConsensusXMLFile.html#a963bc7db375d58bd099601271cc7a011">OpenMS::ConsensusXMLFile::pep_hit_</a></div><div class="ttdeci">PeptideHit pep_hit_</div><div class="ttdoc">Temporary peptide hit. </div><div class="ttdef"><b>Definition:</b> ConsensusXMLFile.h:131</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="classOpenMS_1_1ConsensusXMLFile_html_ab59916b51e0840799c0a78ed04d7f859"><div class="ttname"><a href="classOpenMS_1_1ConsensusXMLFile.html#ab59916b51e0840799c0a78ed04d7f859">OpenMS::ConsensusXMLFile::pep_id_</a></div><div class="ttdeci">PeptideIdentification pep_id_</div><div class="ttdoc">Temporary peptide ProteinIdentification. </div><div class="ttdef"><b>Definition:</b> ConsensusXMLFile.h:127</div></div>
<div class="ttc" id="classOpenMS_1_1ConsensusXMLFile_html_a15e5e3bc144b437972738bf1d168b741"><div class="ttname"><a href="classOpenMS_1_1ConsensusXMLFile.html#a15e5e3bc144b437972738bf1d168b741">OpenMS::ConsensusXMLFile::accession_to_id_</a></div><div class="ttdeci">Map< String, Size > accession_to_id_</div><div class="ttdoc">Map from search identifier concatenated with protein accession to id. </div><div class="ttdef"><b>Definition:</b> ConsensusXMLFile.h:135</div></div>
<div class="ttc" id="classOpenMS_1_1ConsensusXMLFile_html_a65fe117944045e89e6add20e3f7ba912"><div class="ttname"><a href="classOpenMS_1_1ConsensusXMLFile.html#a65fe117944045e89e6add20e3f7ba912">OpenMS::ConsensusXMLFile::identifier_id_</a></div><div class="ttdeci">Map< String, String > identifier_id_</div><div class="ttdoc">Map from identification run identifier to file xs:id (for linking peptide identifications to the corr...</div><div class="ttdef"><b>Definition:</b> ConsensusXMLFile.h:137</div></div>
<div class="ttc" id="classOpenMS_1_1ConsensusXMLFile_html_a8e17f7a3517f0ea0f31fd4c9d7608e3c"><div class="ttname"><a href="classOpenMS_1_1ConsensusXMLFile.html#a8e17f7a3517f0ea0f31fd4c9d7608e3c">OpenMS::ConsensusXMLFile::progress_</a></div><div class="ttdeci">UInt progress_</div><div class="ttdef"><b>Definition:</b> ConsensusXMLFile.h:143</div></div>
<div class="ttc" id="classOpenMS_1_1ConsensusXMLFile_html"><div class="ttname"><a href="classOpenMS_1_1ConsensusXMLFile.html">OpenMS::ConsensusXMLFile</a></div><div class="ttdoc">This class provides Input functionality for ConsensusMaps and Output functionality for alignments and...</div><div class="ttdef"><b>Definition:</b> ConsensusXMLFile.h:59</div></div>
<div class="ttc" id="classOpenMS_1_1DPosition_html"><div class="ttname"><a href="classOpenMS_1_1DPosition.html">OpenMS::DPosition< 2 ></a></div></div>
<div class="ttc" id="classOpenMS_1_1PeptideHit_html"><div class="ttname"><a href="classOpenMS_1_1PeptideHit.html">OpenMS::PeptideHit</a></div><div class="ttdoc">Representation of a peptide hit. </div><div class="ttdef"><b>Definition:</b> PeptideHit.h:54</div></div>
<div class="ttc" id="XMLFile_8h_html"><div class="ttname"><a href="XMLFile_8h.html">XMLFile.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1ConsensusXMLFile_html_ad23fa42c762a035786d56a07e2f1ea16"><div class="ttname"><a href="classOpenMS_1_1ConsensusXMLFile.html#ad23fa42c762a035786d56a07e2f1ea16">OpenMS::ConsensusXMLFile::proteinid_to_accession_</a></div><div class="ttdeci">Map< String, String > proteinid_to_accession_</div><div class="ttdoc">Map from protein id to accession. </div><div class="ttdef"><b>Definition:</b> ConsensusXMLFile.h:133</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_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_1ConsensusXMLFile_html_a05fe9910cacd8b17b3c6ac120135a6fc"><div class="ttname"><a href="classOpenMS_1_1ConsensusXMLFile.html#a05fe9910cacd8b17b3c6ac120135a6fc">OpenMS::ConsensusXMLFile::it_</a></div><div class="ttdeci">DoubleReal it_</div><div class="ttdef"><b>Definition:</b> ConsensusXMLFile.h:119</div></div>
<div class="ttc" id="classOpenMS_1_1ProgressLogger_html"><div class="ttname"><a href="classOpenMS_1_1ProgressLogger.html">OpenMS::ProgressLogger</a></div><div class="ttdoc">Base class for all classes that want to report their progess. </div><div class="ttdef"><b>Definition:</b> ProgressLogger.h:56</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1XMLFile_html"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1XMLFile.html">OpenMS::Internal::XMLFile</a></div><div class="ttdoc">Base class for loading/storing XML files that have a handler derived from XMLHandler. </div><div class="ttdef"><b>Definition:</b> XMLFile.h:51</div></div>
<div class="ttc" id="classOpenMS_1_1ConsensusXMLFile_html_a23a7355f9a0e61f3990a763f0fa7c528"><div class="ttname"><a href="classOpenMS_1_1ConsensusXMLFile.html#a23a7355f9a0e61f3990a763f0fa7c528">OpenMS::ConsensusXMLFile::last_meta_</a></div><div class="ttdeci">MetaInfoInterface * last_meta_</div><div class="ttdoc">Pointer to last read object as a MetaInfoInterface, or null. </div><div class="ttdef"><b>Definition:</b> ConsensusXMLFile.h:123</div></div>
<div class="ttc" id="classOpenMS_1_1PeakFileOptions_html"><div class="ttname"><a href="classOpenMS_1_1PeakFileOptions.html">OpenMS::PeakFileOptions</a></div><div class="ttdoc">Options for loading files containing peak data. </div><div class="ttdef"><b>Definition:</b> PeakFileOptions.h:47</div></div>
<div class="ttc" id="classOpenMS_1_1ConsensusXMLFile_html_a590ed25661a837bfedb38402e2c50b47"><div class="ttname"><a href="classOpenMS_1_1ConsensusXMLFile.html#a590ed25661a837bfedb38402e2c50b47">OpenMS::ConsensusXMLFile::pos_</a></div><div class="ttdeci">DPosition< 2 > pos_</div><div class="ttdef"><b>Definition:</b> ConsensusXMLFile.h:118</div></div>
<div class="ttc" id="classOpenMS_1_1Map_html"><div class="ttname"><a href="classOpenMS_1_1Map.html">OpenMS::Map</a></div><div class="ttdoc">Map class based on the STL map (containing serveral convenience functions) </div><div class="ttdef"><b>Definition:</b> Map.h:50</div></div>
<div class="ttc" id="XMLHandler_8h_html"><div class="ttname"><a href="XMLHandler_8h.html">XMLHandler.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1ConsensusFeature_html"><div class="ttname"><a href="classOpenMS_1_1ConsensusFeature.html">OpenMS::ConsensusFeature</a></div><div class="ttdoc">A 2-dimensional consensus feature. </div><div class="ttdef"><b>Definition:</b> ConsensusFeature.h:59</div></div>
<div class="ttc" id="classOpenMS_1_1PeptideIdentification_html"><div class="ttname"><a href="classOpenMS_1_1PeptideIdentification.html">OpenMS::PeptideIdentification</a></div><div class="ttdoc">Represents the peptide hits for a spectrum. </div><div class="ttdef"><b>Definition:</b> PeptideIdentification.h:63</div></div>
</div><!-- fragment --></div><!-- contents -->
<HR style="height:1px; border:none; border-top:1px solid #c0c0c0;">
<TABLE width="100%" border="0">
<TR>
<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:12 using doxygen 1.8.5</font></TD>
</TR>
</TABLE>
</BODY>
</HTML>
|
