File: DTA2DFile_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 (351 lines) | stat: -rw-r--r-- 54,959 bytes parent folder | download 
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
 
<HTML>
<HEAD>
<TITLE>DTA2DFile.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_d1695c75ee0aa48d87e52f45c7decd7a.html">FORMAT</a></li>  </ul>
</div>
</div><!-- top -->
<div class="header">
  <div class="headertitle">
<div class="title">DTA2DFile.h</div>  </div>
</div><!--header-->
<div class="contents">
<a href="DTA2DFile_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: Andreas Bertsch $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160;<span class="comment">// $Authors: Marc Sturm $</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_FORMAT_DTA2DFILE_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_FORMAT_DTA2DFILE_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="String_8h.html">OpenMS/DATASTRUCTURES/String.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="PeakFileOptions_8h.html">OpenMS/FORMAT/OPTIONS/PeakFileOptions.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="ProgressLogger_8h.html">OpenMS/CONCEPT/ProgressLogger.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;fstream&gt;</span></div>
<div class="line"><a name="l00043"></a><span class="lineno">   43</span>&#160;<span class="preprocessor">#include &lt;iostream&gt;</span></div>
<div class="line"><a name="l00044"></a><span class="lineno">   44</span>&#160;</div>
<div class="line"><a name="l00045"></a><span class="lineno">   45</span>&#160;<span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00046"></a><span class="lineno">   46</span>&#160;{</div>
<div class="line"><a name="l00047"></a><span class="lineno">   47</span>&#160;  <span class="keyword">class </span>String;</div>
<div class="line"><a name="l00064"></a><span class="lineno"><a class="line" href="classOpenMS_1_1DTA2DFile.html">   64</a></span>&#160;  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1DTA2DFile.html">DTA2DFile</a> :</div>
<div class="line"><a name="l00065"></a><span class="lineno">   65</span>&#160;    <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a></div>
<div class="line"><a name="l00066"></a><span class="lineno">   66</span>&#160;  {</div>
<div class="line"><a name="l00067"></a><span class="lineno">   67</span>&#160;<span class="keyword">private</span>:</div>
<div class="line"><a name="l00068"></a><span class="lineno"><a class="line" href="classOpenMS_1_1DTA2DFile.html#a654a0b5941d937e303c64bc9e732baec">   68</a></span>&#160;    <a class="code" href="classOpenMS_1_1PeakFileOptions.html">PeakFileOptions</a> <a class="code" href="classOpenMS_1_1DTA2DFile.html#a654a0b5941d937e303c64bc9e732baec">options_</a>;</div>
<div class="line"><a name="l00069"></a><span class="lineno">   69</span>&#160;</div>
<div class="line"><a name="l00070"></a><span class="lineno">   70</span>&#160;<span class="keyword">public</span>:</div>
<div class="line"><a name="l00071"></a><span class="lineno">   71</span>&#160;</div>
<div class="line"><a name="l00074"></a><span class="lineno">   74</span>&#160;    <a class="code" href="classOpenMS_1_1DTA2DFile.html">DTA2DFile</a>();</div>
<div class="line"><a name="l00077"></a><span class="lineno">   77</span>&#160;    ~<a class="code" href="classOpenMS_1_1DTA2DFile.html">DTA2DFile</a>();</div>
<div class="line"><a name="l00079"></a><span class="lineno">   79</span>&#160;</div>
<div class="line"><a name="l00081"></a><span class="lineno">   81</span>&#160;    <a class="code" href="classOpenMS_1_1PeakFileOptions.html">PeakFileOptions</a> &amp; getOptions();</div>
<div class="line"><a name="l00082"></a><span class="lineno">   82</span>&#160;</div>
<div class="line"><a name="l00084"></a><span class="lineno">   84</span>&#160;    <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1PeakFileOptions.html">PeakFileOptions</a> &amp; getOptions() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00085"></a><span class="lineno">   85</span>&#160;</div>
<div class="line"><a name="l00094"></a><span class="lineno">   94</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">typename</span> MapType&gt;</div>
<div class="line"><a name="l00095"></a><span class="lineno"><a class="line" href="classOpenMS_1_1DTA2DFile.html#aed378b9a389ec00fa2b559bf7d3b710b">   95</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1DTA2DFile.html#aed378b9a389ec00fa2b559bf7d3b710b">load</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; filename, MapType &amp; map)</div>
<div class="line"><a name="l00096"></a><span class="lineno">   96</span>&#160;    {</div>
<div class="line"><a name="l00097"></a><span class="lineno">   97</span>&#160;      startProgress(0, 0, <span class="stringliteral">&quot;loading DTA2D file&quot;</span>);</div>
<div class="line"><a name="l00098"></a><span class="lineno">   98</span>&#160;</div>
<div class="line"><a name="l00099"></a><span class="lineno">   99</span>&#160;      <span class="comment">//try to open file</span></div>
<div class="line"><a name="l00100"></a><span class="lineno">  100</span>&#160;      std::ifstream is(filename.c_str());</div>
<div class="line"><a name="l00101"></a><span class="lineno">  101</span>&#160;      <span class="keywordflow">if</span> (!is)</div>
<div class="line"><a name="l00102"></a><span class="lineno">  102</span>&#160;      {</div>
<div class="line"><a name="l00103"></a><span class="lineno">  103</span>&#160;        <span class="keywordflow">throw</span> <a class="code" href="classOpenMS_1_1Exception_1_1FileNotFound.html">Exception::FileNotFound</a>(__FILE__, __LINE__, __PRETTY_FUNCTION__, filename);</div>
<div class="line"><a name="l00104"></a><span class="lineno">  104</span>&#160;      }</div>
<div class="line"><a name="l00105"></a><span class="lineno">  105</span>&#160;</div>
<div class="line"><a name="l00106"></a><span class="lineno">  106</span>&#160;      map.reset();</div>
<div class="line"><a name="l00107"></a><span class="lineno">  107</span>&#160;</div>
<div class="line"><a name="l00108"></a><span class="lineno">  108</span>&#160;      <span class="comment">//set DocumentIdentifier</span></div>
<div class="line"><a name="l00109"></a><span class="lineno">  109</span>&#160;      map.setLoadedFileType(filename);</div>
<div class="line"><a name="l00110"></a><span class="lineno">  110</span>&#160;      map.setLoadedFilePath(filename);</div>
<div class="line"><a name="l00111"></a><span class="lineno">  111</span>&#160;</div>
<div class="line"><a name="l00112"></a><span class="lineno">  112</span>&#160;      <span class="comment">// temporary variables to store the data in</span></div>
<div class="line"><a name="l00113"></a><span class="lineno">  113</span>&#160;      std::vector&lt;String&gt; strings(3);</div>
<div class="line"><a name="l00114"></a><span class="lineno">  114</span>&#160;      <span class="keyword">typename</span> MapType::SpectrumType spec;</div>
<div class="line"><a name="l00115"></a><span class="lineno">  115</span>&#160;      spec.setRT(-1.0);       <span class="comment">//to make sure the first RT is different from the the initialized value</span></div>
<div class="line"><a name="l00116"></a><span class="lineno">  116</span>&#160;      <span class="keyword">typename</span> <a class="code" href="namespaceOpenMS.html#a013338b7bdbb5c3b4c78666656070e23">MapType::SpectrumType::PeakType</a> p;</div>
<div class="line"><a name="l00117"></a><span class="lineno">  117</span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> rt(0.0);</div>
<div class="line"><a name="l00118"></a><span class="lineno">  118</span>&#160;      <span class="keywordtype">char</span> delimiter;</div>
<div class="line"><a name="l00119"></a><span class="lineno">  119</span>&#160;</div>
<div class="line"><a name="l00120"></a><span class="lineno">  120</span>&#160;      <span class="comment">// default dimension of the data</span></div>
<div class="line"><a name="l00121"></a><span class="lineno">  121</span>&#160;      <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> rt_dim = 0;</div>
<div class="line"><a name="l00122"></a><span class="lineno">  122</span>&#160;      <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> mz_dim = 1;</div>
<div class="line"><a name="l00123"></a><span class="lineno">  123</span>&#160;      <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> int_dim = 2;</div>
<div class="line"><a name="l00124"></a><span class="lineno">  124</span>&#160;</div>
<div class="line"><a name="l00125"></a><span class="lineno">  125</span>&#160;      <span class="comment">//RT unit (default is seconds)</span></div>
<div class="line"><a name="l00126"></a><span class="lineno">  126</span>&#160;      <span class="keywordtype">bool</span> time_in_minutes = <span class="keyword">false</span>;</div>
<div class="line"><a name="l00127"></a><span class="lineno">  127</span>&#160;</div>
<div class="line"><a name="l00128"></a><span class="lineno">  128</span>&#160;      <span class="comment">// string to store the current line in</span></div>
<div class="line"><a name="l00129"></a><span class="lineno">  129</span>&#160;      <a class="code" href="classOpenMS_1_1String.html">String</a> line;</div>
<div class="line"><a name="l00130"></a><span class="lineno">  130</span>&#160;</div>
<div class="line"><a name="l00131"></a><span class="lineno">  131</span>&#160;      <span class="comment">// native ID (numbers from 0)</span></div>
<div class="line"><a name="l00132"></a><span class="lineno">  132</span>&#160;      <a class="code" href="classunsigned_01int.html">UInt</a> native_id = 0;</div>
<div class="line"><a name="l00133"></a><span class="lineno">  133</span>&#160;</div>
<div class="line"><a name="l00134"></a><span class="lineno">  134</span>&#160;      <span class="comment">// line number counter</span></div>
<div class="line"><a name="l00135"></a><span class="lineno">  135</span>&#160;      <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> line_number = 0;</div>
<div class="line"><a name="l00136"></a><span class="lineno">  136</span>&#160;</div>
<div class="line"><a name="l00137"></a><span class="lineno">  137</span>&#160;      <span class="keywordflow">while</span> (getline(is, line, <span class="charliteral">&#39;\n&#39;</span>))</div>
<div class="line"><a name="l00138"></a><span class="lineno">  138</span>&#160;      {</div>
<div class="line"><a name="l00139"></a><span class="lineno">  139</span>&#160;        ++line_number;</div>
<div class="line"><a name="l00140"></a><span class="lineno">  140</span>&#160;        line.<a class="code" href="classOpenMS_1_1String.html#a86864c88ee12eb322f1645f238c1dbe5">trim</a>();</div>
<div class="line"><a name="l00141"></a><span class="lineno">  141</span>&#160;</div>
<div class="line"><a name="l00142"></a><span class="lineno">  142</span>&#160;        <span class="keywordflow">if</span> (line.empty()) <span class="keywordflow">continue</span>;</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;        <span class="comment">//test which delimiter is used in the line</span></div>
<div class="line"><a name="l00145"></a><span class="lineno">  145</span>&#160;        <span class="keywordflow">if</span> (line.<a class="code" href="classOpenMS_1_1String.html#a58599d37159ebc08a654fb2d25be92fe">has</a>(<span class="charliteral">&#39;\t&#39;</span>))</div>
<div class="line"><a name="l00146"></a><span class="lineno">  146</span>&#160;        {</div>
<div class="line"><a name="l00147"></a><span class="lineno">  147</span>&#160;          delimiter = <span class="charliteral">&#39;\t&#39;</span>;</div>
<div class="line"><a name="l00148"></a><span class="lineno">  148</span>&#160;        }</div>
<div class="line"><a name="l00149"></a><span class="lineno">  149</span>&#160;        <span class="keywordflow">else</span></div>
<div class="line"><a name="l00150"></a><span class="lineno">  150</span>&#160;        {</div>
<div class="line"><a name="l00151"></a><span class="lineno">  151</span>&#160;          delimiter = <span class="charliteral">&#39; &#39;</span>;</div>
<div class="line"><a name="l00152"></a><span class="lineno">  152</span>&#160;        }</div>
<div class="line"><a name="l00153"></a><span class="lineno">  153</span>&#160;</div>
<div class="line"><a name="l00154"></a><span class="lineno">  154</span>&#160;        <span class="comment">//is header line</span></div>
<div class="line"><a name="l00155"></a><span class="lineno">  155</span>&#160;        <span class="keywordflow">if</span> (line.<a class="code" href="classOpenMS_1_1String.html#ae1870a969417d19a33f225046a66a58d">hasPrefix</a>(<span class="stringliteral">&quot;#&quot;</span>))</div>
<div class="line"><a name="l00156"></a><span class="lineno">  156</span>&#160;        {</div>
<div class="line"><a name="l00157"></a><span class="lineno">  157</span>&#160;          line = line.<a class="code" href="classOpenMS_1_1String.html#a226b41d565aa586bd45aa7d046608511">substr</a>(1).<a class="code" href="classOpenMS_1_1String.html#a86864c88ee12eb322f1645f238c1dbe5">trim</a>();</div>
<div class="line"><a name="l00158"></a><span class="lineno">  158</span>&#160;          line.<a class="code" href="classOpenMS_1_1String.html#ae580d960e12c7f0ebc5c95931cf39ad5">split</a>(delimiter, strings);</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">  160</span>&#160;          <span class="comment">// flags to check if dimension is set correctly</span></div>
<div class="line"><a name="l00161"></a><span class="lineno">  161</span>&#160;          <span class="keywordtype">bool</span> rt_set = <span class="keyword">false</span>;</div>
<div class="line"><a name="l00162"></a><span class="lineno">  162</span>&#160;          <span class="keywordtype">bool</span> mz_set = <span class="keyword">false</span>;</div>
<div class="line"><a name="l00163"></a><span class="lineno">  163</span>&#160;          <span class="keywordtype">bool</span> int_set = <span class="keyword">false</span>;</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;          <span class="comment">//assign new order</span></div>
<div class="line"><a name="l00166"></a><span class="lineno">  166</span>&#160;          <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i &lt; 3; ++i)</div>
<div class="line"><a name="l00167"></a><span class="lineno">  167</span>&#160;          {</div>
<div class="line"><a name="l00168"></a><span class="lineno">  168</span>&#160;            <span class="keywordflow">if</span> (strings[i] == <span class="stringliteral">&quot;RT&quot;</span> || strings[i] == <span class="stringliteral">&quot;RETENTION_TIME&quot;</span> || strings[i] == <span class="stringliteral">&quot;MASS-TO-CHARGE&quot;</span> || strings[i] == <span class="stringliteral">&quot;IT&quot;</span> || strings[i] == <span class="stringliteral">&quot;INTENSITY&quot;</span>)</div>
<div class="line"><a name="l00169"></a><span class="lineno">  169</span>&#160;            {</div>
<div class="line"><a name="l00170"></a><span class="lineno">  170</span>&#160;              std::cerr &lt;&lt; <span class="stringliteral">&quot;Warning: This file contains the deprecated keyword &#39;&quot;</span> &lt;&lt; strings[i] &lt;&lt; <span class="stringliteral">&quot;&#39;.&quot;</span> &lt;&lt; <span class="stringliteral">&quot;\n&quot;</span>;</div>
<div class="line"><a name="l00171"></a><span class="lineno">  171</span>&#160;              std::cerr &lt;&lt; <span class="stringliteral">&quot;         Please use only the new keywords SEC/MIN, MZ, INT.&quot;</span> &lt;&lt; <span class="stringliteral">&quot;\n&quot;</span>;</div>
<div class="line"><a name="l00172"></a><span class="lineno">  172</span>&#160;            }</div>
<div class="line"><a name="l00173"></a><span class="lineno">  173</span>&#160;            <span class="keywordflow">if</span> ((strings[i] == <span class="stringliteral">&quot;SEC&quot;</span> || strings[i] == <span class="stringliteral">&quot;RT&quot;</span> || strings[i] == <span class="stringliteral">&quot;RETENTION_TIME&quot;</span>) &amp;&amp; rt_set == <span class="keyword">false</span>)</div>
<div class="line"><a name="l00174"></a><span class="lineno">  174</span>&#160;            {</div>
<div class="line"><a name="l00175"></a><span class="lineno">  175</span>&#160;              rt_dim = i;</div>
<div class="line"><a name="l00176"></a><span class="lineno">  176</span>&#160;              rt_set = <span class="keyword">true</span>;</div>
<div class="line"><a name="l00177"></a><span class="lineno">  177</span>&#160;            }</div>
<div class="line"><a name="l00178"></a><span class="lineno">  178</span>&#160;            <span class="keywordflow">else</span> <span class="keywordflow">if</span> ((strings[i] == <span class="stringliteral">&quot;MIN&quot;</span>) &amp;&amp; rt_set == <span class="keyword">false</span>)</div>
<div class="line"><a name="l00179"></a><span class="lineno">  179</span>&#160;            {</div>
<div class="line"><a name="l00180"></a><span class="lineno">  180</span>&#160;              rt_dim = i;</div>
<div class="line"><a name="l00181"></a><span class="lineno">  181</span>&#160;              rt_set = <span class="keyword">true</span>;</div>
<div class="line"><a name="l00182"></a><span class="lineno">  182</span>&#160;              time_in_minutes = <span class="keyword">true</span>;</div>
<div class="line"><a name="l00183"></a><span class="lineno">  183</span>&#160;            }</div>
<div class="line"><a name="l00184"></a><span class="lineno">  184</span>&#160;            <span class="keywordflow">else</span> <span class="keywordflow">if</span> ((strings[i] == <span class="stringliteral">&quot;MZ&quot;</span> || strings[i] == <span class="stringliteral">&quot;MASS-TO-CHARGE&quot;</span>) &amp;&amp; mz_set == <span class="keyword">false</span>)</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;              mz_dim = i;</div>
<div class="line"><a name="l00187"></a><span class="lineno">  187</span>&#160;              mz_set = <span class="keyword">true</span>;</div>
<div class="line"><a name="l00188"></a><span class="lineno">  188</span>&#160;            }</div>
<div class="line"><a name="l00189"></a><span class="lineno">  189</span>&#160;            <span class="keywordflow">else</span> <span class="keywordflow">if</span> ((strings[i] == <span class="stringliteral">&quot;INT&quot;</span> || strings[i] == <span class="stringliteral">&quot;IT&quot;</span> || strings[i] == <span class="stringliteral">&quot;INTENSITY&quot;</span>) &amp;&amp; int_set == <span class="keyword">false</span>)</div>
<div class="line"><a name="l00190"></a><span class="lineno">  190</span>&#160;            {</div>
<div class="line"><a name="l00191"></a><span class="lineno">  191</span>&#160;              int_dim = i;</div>
<div class="line"><a name="l00192"></a><span class="lineno">  192</span>&#160;              int_set = <span class="keyword">true</span>;</div>
<div class="line"><a name="l00193"></a><span class="lineno">  193</span>&#160;            }</div>
<div class="line"><a name="l00194"></a><span class="lineno">  194</span>&#160;            <span class="keywordflow">else</span></div>
<div class="line"><a name="l00195"></a><span class="lineno">  195</span>&#160;            {</div>
<div class="line"><a name="l00196"></a><span class="lineno">  196</span>&#160;              <span class="keywordflow">throw</span> <a class="code" href="classOpenMS_1_1Exception_1_1ParseError.html">Exception::ParseError</a>(__FILE__, __LINE__, __PRETTY_FUNCTION__, <span class="stringliteral">&quot;Misformatted header line!&quot;</span>, filename);</div>
<div class="line"><a name="l00197"></a><span class="lineno">  197</span>&#160;            }</div>
<div class="line"><a name="l00198"></a><span class="lineno">  198</span>&#160;          }</div>
<div class="line"><a name="l00199"></a><span class="lineno">  199</span>&#160;          <span class="keywordflow">continue</span>;</div>
<div class="line"><a name="l00200"></a><span class="lineno">  200</span>&#160;        }</div>
<div class="line"><a name="l00201"></a><span class="lineno">  201</span>&#160;</div>
<div class="line"><a name="l00202"></a><span class="lineno">  202</span>&#160;        <span class="keywordflow">try</span></div>
<div class="line"><a name="l00203"></a><span class="lineno">  203</span>&#160;        {</div>
<div class="line"><a name="l00204"></a><span class="lineno">  204</span>&#160;          line.<a class="code" href="classOpenMS_1_1String.html#ae580d960e12c7f0ebc5c95931cf39ad5">split</a>(delimiter, strings);</div>
<div class="line"><a name="l00205"></a><span class="lineno">  205</span>&#160;          <span class="keywordflow">if</span> (strings.size() != 3)</div>
<div class="line"><a name="l00206"></a><span class="lineno">  206</span>&#160;          {</div>
<div class="line"><a name="l00207"></a><span class="lineno">  207</span>&#160;            <span class="keywordflow">throw</span> <a class="code" href="classOpenMS_1_1Exception_1_1ParseError.html">Exception::ParseError</a>(__FILE__, __LINE__, __PRETTY_FUNCTION__, std::string(<span class="stringliteral">&quot;Bad data line (&quot;</span> + <a class="code" href="classOpenMS_1_1String.html">String</a>(line_number) + <span class="stringliteral">&quot;): \&quot;&quot;</span>) + line + <span class="stringliteral">&quot;\&quot; (got  &quot;</span> + <a class="code" href="classOpenMS_1_1String.html">String</a>(strings.size()) + <span class="stringliteral">&quot;, expected 3 entries)&quot;</span>, filename);</div>
<div class="line"><a name="l00208"></a><span class="lineno">  208</span>&#160;          }</div>
<div class="line"><a name="l00209"></a><span class="lineno">  209</span>&#160;          p.setIntensity(strings[int_dim].toFloat());</div>
<div class="line"><a name="l00210"></a><span class="lineno">  210</span>&#160;          p.setMZ(strings[mz_dim].toDouble());</div>
<div class="line"><a name="l00211"></a><span class="lineno">  211</span>&#160;          rt = (strings[rt_dim].toDouble()) * (time_in_minutes ? 60.0 : 1.0);</div>
<div class="line"><a name="l00212"></a><span class="lineno">  212</span>&#160;        }</div>
<div class="line"><a name="l00213"></a><span class="lineno">  213</span>&#160;        <span class="comment">// conversion to double or something else could have gone wrong</span></div>
<div class="line"><a name="l00214"></a><span class="lineno">  214</span>&#160;        <span class="keywordflow">catch</span> (<a class="code" href="classOpenMS_1_1Exception_1_1BaseException.html">Exception::BaseException</a> &amp; <span class="comment">/*e*/</span>)</div>
<div class="line"><a name="l00215"></a><span class="lineno">  215</span>&#160;        {</div>
<div class="line"><a name="l00216"></a><span class="lineno">  216</span>&#160;          <span class="keywordflow">throw</span> <a class="code" href="classOpenMS_1_1Exception_1_1ParseError.html">Exception::ParseError</a>(__FILE__, __LINE__, __PRETTY_FUNCTION__, std::string(<span class="stringliteral">&quot;Bad data line (&quot;</span> + <a class="code" href="classOpenMS_1_1String.html">String</a>(line_number) + <span class="stringliteral">&quot;): \&quot;&quot;</span>) + line + <span class="stringliteral">&quot;\&quot;&quot;</span>, filename);</div>
<div class="line"><a name="l00217"></a><span class="lineno">  217</span>&#160;        }</div>
<div class="line"><a name="l00218"></a><span class="lineno">  218</span>&#160;</div>
<div class="line"><a name="l00219"></a><span class="lineno">  219</span>&#160;        <span class="comment">// Retention time changed -&gt; new Spectrum</span></div>
<div class="line"><a name="l00220"></a><span class="lineno">  220</span>&#160;        <span class="keywordflow">if</span> (fabs(rt - spec.getRT()) &gt; 0.0001)</div>
<div class="line"><a name="l00221"></a><span class="lineno">  221</span>&#160;        {</div>
<div class="line"><a name="l00222"></a><span class="lineno">  222</span>&#160;          <span class="keywordflow">if</span> (spec.size() != 0</div>
<div class="line"><a name="l00223"></a><span class="lineno">  223</span>&#160;             &amp;&amp;</div>
<div class="line"><a name="l00224"></a><span class="lineno">  224</span>&#160;              (!options_.hasRTRange() || options_.getRTRange().encloses(<a class="code" href="classOpenMS_1_1DPosition.html">DPosition&lt;1&gt;</a>(spec.getRT()))))                <span class="comment">// RT restriction fulfilled</span></div>
<div class="line"><a name="l00225"></a><span class="lineno">  225</span>&#160;          {</div>
<div class="line"><a name="l00226"></a><span class="lineno">  226</span>&#160;            map.addSpectrum(spec);</div>
<div class="line"><a name="l00227"></a><span class="lineno">  227</span>&#160;          }</div>
<div class="line"><a name="l00228"></a><span class="lineno">  228</span>&#160;          setProgress(0);</div>
<div class="line"><a name="l00229"></a><span class="lineno">  229</span>&#160;          spec.clear(<span class="keyword">true</span>);</div>
<div class="line"><a name="l00230"></a><span class="lineno">  230</span>&#160;          spec.setRT(rt);</div>
<div class="line"><a name="l00231"></a><span class="lineno">  231</span>&#160;          spec.setNativeID(<a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;index=&quot;</span>) + native_id);</div>
<div class="line"><a name="l00232"></a><span class="lineno">  232</span>&#160;          ++native_id;</div>
<div class="line"><a name="l00233"></a><span class="lineno">  233</span>&#160;        }</div>
<div class="line"><a name="l00234"></a><span class="lineno">  234</span>&#160;</div>
<div class="line"><a name="l00235"></a><span class="lineno">  235</span>&#160;        <span class="comment">//Skip peaks with invalid m/z or intensity value</span></div>
<div class="line"><a name="l00236"></a><span class="lineno">  236</span>&#160;        <span class="keywordflow">if</span> (</div>
<div class="line"><a name="l00237"></a><span class="lineno">  237</span>&#160;          (!options_.hasMZRange() || options_.getMZRange().encloses(<a class="code" href="classOpenMS_1_1DPosition.html">DPosition&lt;1&gt;</a>(p.getMZ())))</div>
<div class="line"><a name="l00238"></a><span class="lineno">  238</span>&#160;           &amp;&amp;</div>
<div class="line"><a name="l00239"></a><span class="lineno">  239</span>&#160;          (!options_.hasIntensityRange() || options_.getIntensityRange().encloses(<a class="code" href="classOpenMS_1_1DPosition.html">DPosition&lt;1&gt;</a>(p.getIntensity())))</div>
<div class="line"><a name="l00240"></a><span class="lineno">  240</span>&#160;          )</div>
<div class="line"><a name="l00241"></a><span class="lineno">  241</span>&#160;        {</div>
<div class="line"><a name="l00242"></a><span class="lineno">  242</span>&#160;          spec.push_back(p);</div>
<div class="line"><a name="l00243"></a><span class="lineno">  243</span>&#160;        }</div>
<div class="line"><a name="l00244"></a><span class="lineno">  244</span>&#160;      }</div>
<div class="line"><a name="l00245"></a><span class="lineno">  245</span>&#160;</div>
<div class="line"><a name="l00246"></a><span class="lineno">  246</span>&#160;      <span class="comment">// add last Spectrum</span></div>
<div class="line"><a name="l00247"></a><span class="lineno">  247</span>&#160;      <span class="keywordflow">if</span> (</div>
<div class="line"><a name="l00248"></a><span class="lineno">  248</span>&#160;        spec.size() != 0</div>
<div class="line"><a name="l00249"></a><span class="lineno">  249</span>&#160;         &amp;&amp;</div>
<div class="line"><a name="l00250"></a><span class="lineno">  250</span>&#160;        (!options_.hasRTRange() || options_.getRTRange().encloses(<a class="code" href="classOpenMS_1_1DPosition.html">DPosition&lt;1&gt;</a>(spec.getRT())))             <span class="comment">// RT restriction fulfilled</span></div>
<div class="line"><a name="l00251"></a><span class="lineno">  251</span>&#160;        )</div>
<div class="line"><a name="l00252"></a><span class="lineno">  252</span>&#160;      {</div>
<div class="line"><a name="l00253"></a><span class="lineno">  253</span>&#160;        map.addSpectrum(spec);</div>
<div class="line"><a name="l00254"></a><span class="lineno">  254</span>&#160;      }</div>
<div class="line"><a name="l00255"></a><span class="lineno">  255</span>&#160;</div>
<div class="line"><a name="l00256"></a><span class="lineno">  256</span>&#160;      is.close();</div>
<div class="line"><a name="l00257"></a><span class="lineno">  257</span>&#160;      endProgress();</div>
<div class="line"><a name="l00258"></a><span class="lineno">  258</span>&#160;    }</div>
<div class="line"><a name="l00259"></a><span class="lineno">  259</span>&#160;</div>
<div class="line"><a name="l00267"></a><span class="lineno">  267</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">typename</span> MapType&gt;</div>
<div class="line"><a name="l00268"></a><span class="lineno"><a class="line" href="classOpenMS_1_1DTA2DFile.html#adb795d215478320be7c6130ff7ddf853">  268</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1DTA2DFile.html#adb795d215478320be7c6130ff7ddf853">store</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; filename, <span class="keyword">const</span> MapType &amp; map)<span class="keyword"> const</span></div>
<div class="line"><a name="l00269"></a><span class="lineno">  269</span>&#160;<span class="keyword">    </span>{</div>
<div class="line"><a name="l00270"></a><span class="lineno">  270</span>&#160;      startProgress(0, map.size(), <span class="stringliteral">&quot;storing DTA2D file&quot;</span>);</div>
<div class="line"><a name="l00271"></a><span class="lineno">  271</span>&#160;</div>
<div class="line"><a name="l00272"></a><span class="lineno">  272</span>&#160;      std::ofstream os(filename.c_str());</div>
<div class="line"><a name="l00273"></a><span class="lineno">  273</span>&#160;      <span class="keywordflow">if</span> (!os)</div>
<div class="line"><a name="l00274"></a><span class="lineno">  274</span>&#160;      {</div>
<div class="line"><a name="l00275"></a><span class="lineno">  275</span>&#160;        <span class="keywordflow">throw</span> <a class="code" href="classOpenMS_1_1Exception_1_1UnableToCreateFile.html">Exception::UnableToCreateFile</a>(__FILE__, __LINE__, __PRETTY_FUNCTION__, filename);</div>
<div class="line"><a name="l00276"></a><span class="lineno">  276</span>&#160;      }</div>
<div class="line"><a name="l00277"></a><span class="lineno">  277</span>&#160;</div>
<div class="line"><a name="l00278"></a><span class="lineno">  278</span>&#160;      <span class="comment">// write header</span></div>
<div class="line"><a name="l00279"></a><span class="lineno">  279</span>&#160;      os &lt;&lt; <span class="stringliteral">&quot;#SEC\tMZ\tINT\n&quot;</span>;</div>
<div class="line"><a name="l00280"></a><span class="lineno">  280</span>&#160;</div>
<div class="line"><a name="l00281"></a><span class="lineno">  281</span>&#160;      <span class="comment">// Iterate over all peaks of each spectrum and</span></div>
<div class="line"><a name="l00282"></a><span class="lineno">  282</span>&#160;      <span class="comment">// write one line for each peak of the spectrum.</span></div>
<div class="line"><a name="l00283"></a><span class="lineno">  283</span>&#160;      <a class="code" href="classunsigned_01int.html">UInt</a> count = 0;</div>
<div class="line"><a name="l00284"></a><span class="lineno">  284</span>&#160;      <span class="keywordflow">for</span> (<span class="keyword">typename</span> MapType::const_iterator spec = map.begin(); spec != map.end(); ++spec)</div>
<div class="line"><a name="l00285"></a><span class="lineno">  285</span>&#160;      {</div>
<div class="line"><a name="l00286"></a><span class="lineno">  286</span>&#160;        setProgress(count++);</div>
<div class="line"><a name="l00287"></a><span class="lineno">  287</span>&#160;        <span class="keywordflow">for</span> (<span class="keyword">typename</span> MapType::SpectrumType::ConstIterator it = spec-&gt;begin(); it != spec-&gt;end(); ++it)</div>
<div class="line"><a name="l00288"></a><span class="lineno">  288</span>&#160;        {</div>
<div class="line"><a name="l00289"></a><span class="lineno">  289</span>&#160;          <span class="comment">// Write rt, m/z and intensity.</span></div>
<div class="line"><a name="l00290"></a><span class="lineno">  290</span>&#160;          os &lt;&lt; <a class="code" href="namespaceOpenMS.html#af27ce8637a6a7cc24cc6fcbd3358791d">precisionWrapper</a>(spec-&gt;getRT()) &lt;&lt; <span class="stringliteral">&quot;\t&quot;</span> &lt;&lt; <a class="code" href="namespaceOpenMS.html#af27ce8637a6a7cc24cc6fcbd3358791d">precisionWrapper</a>(it-&gt;getPos()) &lt;&lt; <span class="stringliteral">&quot;\t&quot;</span> &lt;&lt; <a class="code" href="namespaceOpenMS.html#af27ce8637a6a7cc24cc6fcbd3358791d">precisionWrapper</a>(it-&gt;getIntensity()) &lt;&lt; <span class="stringliteral">&quot;\n&quot;</span>;</div>
<div class="line"><a name="l00291"></a><span class="lineno">  291</span>&#160;        }</div>
<div class="line"><a name="l00292"></a><span class="lineno">  292</span>&#160;</div>
<div class="line"><a name="l00293"></a><span class="lineno">  293</span>&#160;      }</div>
<div class="line"><a name="l00294"></a><span class="lineno">  294</span>&#160;      os.close();</div>
<div class="line"><a name="l00295"></a><span class="lineno">  295</span>&#160;      endProgress();</div>
<div class="line"><a name="l00296"></a><span class="lineno">  296</span>&#160;    }</div>
<div class="line"><a name="l00297"></a><span class="lineno">  297</span>&#160;</div>
<div class="line"><a name="l00305"></a><span class="lineno">  305</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">typename</span> MapType&gt;</div>
<div class="line"><a name="l00306"></a><span class="lineno"><a class="line" href="classOpenMS_1_1DTA2DFile.html#a4dc28e36e6da7b6618b255a4e1d82ded">  306</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1DTA2DFile.html#a4dc28e36e6da7b6618b255a4e1d82ded">storeTIC</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; filename, <span class="keyword">const</span> MapType &amp; map)<span class="keyword"> const</span></div>
<div class="line"><a name="l00307"></a><span class="lineno">  307</span>&#160;<span class="keyword">    </span>{</div>
<div class="line"><a name="l00308"></a><span class="lineno">  308</span>&#160;      startProgress(0, map.size(), <span class="stringliteral">&quot;storing DTA2D file&quot;</span>);</div>
<div class="line"><a name="l00309"></a><span class="lineno">  309</span>&#160;</div>
<div class="line"><a name="l00310"></a><span class="lineno">  310</span>&#160;      std::ofstream os(filename.c_str());</div>
<div class="line"><a name="l00311"></a><span class="lineno">  311</span>&#160;      <span class="keywordflow">if</span> (!os)</div>
<div class="line"><a name="l00312"></a><span class="lineno">  312</span>&#160;      {</div>
<div class="line"><a name="l00313"></a><span class="lineno">  313</span>&#160;        <span class="keywordflow">throw</span> <a class="code" href="classOpenMS_1_1Exception_1_1UnableToCreateFile.html">Exception::UnableToCreateFile</a>(__FILE__, __LINE__, __PRETTY_FUNCTION__, filename);</div>
<div class="line"><a name="l00314"></a><span class="lineno">  314</span>&#160;      }</div>
<div class="line"><a name="l00315"></a><span class="lineno">  315</span>&#160;</div>
<div class="line"><a name="l00316"></a><span class="lineno">  316</span>&#160;      <span class="comment">// write header (Always MZ=0 for chromatograms in DTA2D.)</span></div>
<div class="line"><a name="l00317"></a><span class="lineno">  317</span>&#160;      os &lt;&lt; <span class="stringliteral">&quot;#SEC\tMZ\tINT\n&quot;</span>;</div>
<div class="line"><a name="l00318"></a><span class="lineno">  318</span>&#160;</div>
<div class="line"><a name="l00319"></a><span class="lineno">  319</span>&#160;      <span class="keyword">typename</span> MapType::ChromatogramType TIC = map.getTIC();</div>
<div class="line"><a name="l00320"></a><span class="lineno">  320</span>&#160;      <span class="keywordflow">for</span> (<span class="keyword">typename</span> MapType::ChromatogramType::ConstIterator it = TIC.begin(); it != TIC.end(); ++it)</div>
<div class="line"><a name="l00321"></a><span class="lineno">  321</span>&#160;      {</div>
<div class="line"><a name="l00322"></a><span class="lineno">  322</span>&#160;        <span class="comment">// write rt and intensity.</span></div>
<div class="line"><a name="l00323"></a><span class="lineno">  323</span>&#160;        os &lt;&lt; <a class="code" href="namespaceOpenMS.html#af27ce8637a6a7cc24cc6fcbd3358791d">precisionWrapper</a>(it-&gt;getRT()) &lt;&lt; <span class="stringliteral">&quot;\t&quot;</span> &lt;&lt; <a class="code" href="namespaceOpenMS.html#af27ce8637a6a7cc24cc6fcbd3358791d">precisionWrapper</a>(0) &lt;&lt; <span class="stringliteral">&quot;\t&quot;</span> &lt;&lt; <a class="code" href="namespaceOpenMS.html#af27ce8637a6a7cc24cc6fcbd3358791d">precisionWrapper</a>(it-&gt;getIntensity()) &lt;&lt; <span class="stringliteral">&quot;\n&quot;</span>;</div>
<div class="line"><a name="l00324"></a><span class="lineno">  324</span>&#160;      }</div>
<div class="line"><a name="l00325"></a><span class="lineno">  325</span>&#160;</div>
<div class="line"><a name="l00326"></a><span class="lineno">  326</span>&#160;      os.close();</div>
<div class="line"><a name="l00327"></a><span class="lineno">  327</span>&#160;      endProgress();</div>
<div class="line"><a name="l00328"></a><span class="lineno">  328</span>&#160;    }</div>
<div class="line"><a name="l00329"></a><span class="lineno">  329</span>&#160;</div>
<div class="line"><a name="l00330"></a><span class="lineno">  330</span>&#160;  };</div>
<div class="line"><a name="l00331"></a><span class="lineno">  331</span>&#160;</div>
<div class="line"><a name="l00332"></a><span class="lineno">  332</span>&#160;} <span class="comment">// namespace OpenMS</span></div>
<div class="line"><a name="l00333"></a><span class="lineno">  333</span>&#160;</div>
<div class="line"><a name="l00334"></a><span class="lineno">  334</span>&#160;<span class="preprocessor">#endif // OPENMS_FORMAT_DTA2DFILE_H</span></div>
<div class="ttc" id="classOpenMS_1_1DTA2DFile_html"><div class="ttname"><a href="classOpenMS_1_1DTA2DFile.html">OpenMS::DTA2DFile</a></div><div class="ttdoc">DTA2D File adapter. </div><div class="ttdef"><b>Definition:</b> DTA2DFile.h:64</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_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="ProgressLogger_8h_html"><div class="ttname"><a href="ProgressLogger_8h.html">ProgressLogger.h</a></div></div>
<div class="ttc" id="namespaceOpenMS_html_a013338b7bdbb5c3b4c78666656070e23"><div class="ttname"><a href="namespaceOpenMS.html#a013338b7bdbb5c3b4c78666656070e23">OpenMS::PeakType</a></div><div class="ttdeci">Peak2D PeakType</div><div class="ttdef"><b>Definition:</b> MassTrace.h:49</div></div>
<div class="ttc" id="classOpenMS_1_1DTA2DFile_html_a654a0b5941d937e303c64bc9e732baec"><div class="ttname"><a href="classOpenMS_1_1DTA2DFile.html#a654a0b5941d937e303c64bc9e732baec">OpenMS::DTA2DFile::options_</a></div><div class="ttdeci">PeakFileOptions options_</div><div class="ttdef"><b>Definition:</b> DTA2DFile.h:68</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_1Exception_1_1FileNotFound_html"><div class="ttname"><a href="classOpenMS_1_1Exception_1_1FileNotFound.html">OpenMS::Exception::FileNotFound</a></div><div class="ttdoc">File not found exception. </div><div class="ttdef"><b>Definition:</b> Exception.h:524</div></div>
<div class="ttc" id="classOpenMS_1_1String_html_a58599d37159ebc08a654fb2d25be92fe"><div class="ttname"><a href="classOpenMS_1_1String.html#a58599d37159ebc08a654fb2d25be92fe">OpenMS::String::has</a></div><div class="ttdeci">bool has(Byte byte) const </div><div class="ttdoc">true if String contains the byte, false otherwise </div></div>
<div class="ttc" id="classOpenMS_1_1DTA2DFile_html_a4dc28e36e6da7b6618b255a4e1d82ded"><div class="ttname"><a href="classOpenMS_1_1DTA2DFile.html#a4dc28e36e6da7b6618b255a4e1d82ded">OpenMS::DTA2DFile::storeTIC</a></div><div class="ttdeci">void storeTIC(const String &amp;filename, const MapType &amp;map) const </div><div class="ttdoc">Stores the TIC of a map in a DTA2D file. </div><div class="ttdef"><b>Definition:</b> DTA2DFile.h:306</div></div>
<div class="ttc" id="namespaceOpenMS_html_af27ce8637a6a7cc24cc6fcbd3358791d"><div class="ttname"><a href="namespaceOpenMS.html#af27ce8637a6a7cc24cc6fcbd3358791d">OpenMS::precisionWrapper</a></div><div class="ttdeci">const PrecisionWrapper&lt; FloatingPointType &gt; precisionWrapper(const FloatingPointType rhs)</div><div class="ttdoc">Wrapper function that sets the appropriate precision for output temporarily. The original precision i...</div><div class="ttdef"><b>Definition:</b> Types.h:358</div></div>
<div class="ttc" id="classOpenMS_1_1DPosition_html"><div class="ttname"><a href="classOpenMS_1_1DPosition.html">OpenMS::DPosition&lt; 1 &gt;</a></div></div>
<div class="ttc" id="classOpenMS_1_1String_html_a86864c88ee12eb322f1645f238c1dbe5"><div class="ttname"><a href="classOpenMS_1_1String.html#a86864c88ee12eb322f1645f238c1dbe5">OpenMS::String::trim</a></div><div class="ttdeci">String &amp; trim()</div><div class="ttdoc">removes whitespaces (space, tab, line feed, carriage return) at the beginning and the end of the stri...</div></div>
<div class="ttc" id="classOpenMS_1_1DTA2DFile_html_adb795d215478320be7c6130ff7ddf853"><div class="ttname"><a href="classOpenMS_1_1DTA2DFile.html#adb795d215478320be7c6130ff7ddf853">OpenMS::DTA2DFile::store</a></div><div class="ttdeci">void store(const String &amp;filename, const MapType &amp;map) const </div><div class="ttdoc">Stores a map in a DTA2D file. </div><div class="ttdef"><b>Definition:</b> DTA2DFile.h:268</div></div>
<div class="ttc" id="classOpenMS_1_1Exception_1_1BaseException_html"><div class="ttname"><a href="classOpenMS_1_1Exception_1_1BaseException.html">OpenMS::Exception::BaseException</a></div><div class="ttdoc">Exception base class. </div><div class="ttdef"><b>Definition:</b> Exception.h:90</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_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_1Exception_1_1UnableToCreateFile_html"><div class="ttname"><a href="classOpenMS_1_1Exception_1_1UnableToCreateFile.html">OpenMS::Exception::UnableToCreateFile</a></div><div class="ttdoc">Unable to create file exception. </div><div class="ttdef"><b>Definition:</b> Exception.h:622</div></div>
<div class="ttc" id="classOpenMS_1_1String_html_a226b41d565aa586bd45aa7d046608511"><div class="ttname"><a href="classOpenMS_1_1String.html#a226b41d565aa586bd45aa7d046608511">OpenMS::String::substr</a></div><div class="ttdeci">String substr(size_t pos=0, size_t n=npos) const </div><div class="ttdoc">Wrapper for the STL substr() method. Returns a String object with its contents initialized to a subst...</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_1String_html_ae580d960e12c7f0ebc5c95931cf39ad5"><div class="ttname"><a href="classOpenMS_1_1String.html#ae580d960e12c7f0ebc5c95931cf39ad5">OpenMS::String::split</a></div><div class="ttdeci">bool split(const char splitter, std::vector&lt; String &gt; &amp;substrings, bool quote_protect=false) const </div><div class="ttdoc">Splits a string into substrings using splitter as delimiter. </div></div>
<div class="ttc" id="String_8h_html"><div class="ttname"><a href="String_8h.html">String.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1DTA2DFile_html_aed378b9a389ec00fa2b559bf7d3b710b"><div class="ttname"><a href="classOpenMS_1_1DTA2DFile.html#aed378b9a389ec00fa2b559bf7d3b710b">OpenMS::DTA2DFile::load</a></div><div class="ttdeci">void load(const String &amp;filename, MapType &amp;map)</div><div class="ttdoc">Loads a map from a DTA2D file. </div><div class="ttdef"><b>Definition:</b> DTA2DFile.h:95</div></div>
<div class="ttc" id="classOpenMS_1_1String_html_ae1870a969417d19a33f225046a66a58d"><div class="ttname"><a href="classOpenMS_1_1String.html#ae1870a969417d19a33f225046a66a58d">OpenMS::String::hasPrefix</a></div><div class="ttdeci">bool hasPrefix(const String &amp;string) const </div><div class="ttdoc">true if String begins with string, false otherwise </div></div>
<div class="ttc" id="classOpenMS_1_1Exception_1_1ParseError_html"><div class="ttname"><a href="classOpenMS_1_1Exception_1_1ParseError.html">OpenMS::Exception::ParseError</a></div><div class="ttdoc">Parse Error exception. </div><div class="ttdef"><b>Definition:</b> Exception.h:608</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>