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<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>
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<a href="DTAFile_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>
28
<div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="comment">// OpenMS -- Open-Source Mass Spectrometry</span></div>
29
<div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
30
<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>
31
<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>
32
<div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="comment">//</span></div>
33
<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>
34
<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>
35
<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>
36
<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>
37
<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>
38
<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>
39
<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>
40
<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>
41
<div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="comment">// without specific prior written permission.</span></div>
42
<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>
43
<div class="line"><a name="l00017"></a><span class="lineno"> 17</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
44
<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>
45
<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>
46
<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>
47
<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>
48
<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>
49
<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>
50
<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>
51
<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>
52
<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>
53
<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>
54
<div class="line"><a name="l00028"></a><span class="lineno"> 28</span> <span class="comment">// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</span></div>
55
<div class="line"><a name="l00029"></a><span class="lineno"> 29</span> <span class="comment">//</span></div>
56
<div class="line"><a name="l00030"></a><span class="lineno"> 30</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
57
<div class="line"><a name="l00031"></a><span class="lineno"> 31</span> <span class="comment">// $Maintainer: Andreas Bertsch $</span></div>
58
<div class="line"><a name="l00032"></a><span class="lineno"> 32</span> <span class="comment">// $Authors: Marc Sturm $</span></div>
59
<div class="line"><a name="l00033"></a><span class="lineno"> 33</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
60
<div class="line"><a name="l00034"></a><span class="lineno"> 34</span> </div>
61
<div class="line"><a name="l00035"></a><span class="lineno"> 35</span> <span class="preprocessor">#ifndef OPENMS_FORMAT_DTAFILE_H</span></div>
62
<div class="line"><a name="l00036"></a><span class="lineno"> 36</span> <span class="preprocessor"></span><span class="preprocessor">#define OPENMS_FORMAT_DTAFILE_H</span></div>
63
<div class="line"><a name="l00037"></a><span class="lineno"> 37</span> <span class="preprocessor"></span></div>
64
<div class="line"><a name="l00038"></a><span class="lineno"> 38</span> <span class="preprocessor">#include <<a class="code" href="String_8h.html">OpenMS/DATASTRUCTURES/String.h</a>></span></div>
65
<div class="line"><a name="l00039"></a><span class="lineno"> 39</span> <span class="preprocessor">#include <<a class="code" href="Constants_8h.html">OpenMS/CONCEPT/Constants.h</a>></span></div>
66
<div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="preprocessor">#include <<a class="code" href="Precursor_8h.html">OpenMS/METADATA/Precursor.h</a>></span></div>
67
<div class="line"><a name="l00041"></a><span class="lineno"> 41</span> <span class="preprocessor">#include <<a class="code" href="File_8h.html">OpenMS/SYSTEM/File.h</a>></span></div>
68
<div class="line"><a name="l00042"></a><span class="lineno"> 42</span> </div>
69
<div class="line"><a name="l00043"></a><span class="lineno"> 43</span> <span class="preprocessor">#include <fstream></span></div>
70
<div class="line"><a name="l00044"></a><span class="lineno"> 44</span> <span class="preprocessor">#include <vector></span></div>
71
<div class="line"><a name="l00045"></a><span class="lineno"> 45</span> </div>
72
<div class="line"><a name="l00046"></a><span class="lineno"> 46</span> <span class="keyword">namespace </span>OpenMS</div>
73
<div class="line"><a name="l00047"></a><span class="lineno"> 47</span> {</div>
74
<div class="line"><a name="l00058"></a><span class="lineno"><a class="line" href="classOpenMS_1_1DTAFile.html"> 58</a></span>  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1DTAFile.html">DTAFile</a></div>
75
<div class="line"><a name="l00059"></a><span class="lineno"> 59</span>  {</div>
76
<div class="line"><a name="l00060"></a><span class="lineno"> 60</span> <span class="keyword">public</span>:</div>
77
<div class="line"><a name="l00062"></a><span class="lineno"> 62</span>  <a class="code" href="classOpenMS_1_1DTAFile.html">DTAFile</a>();</div>
78
<div class="line"><a name="l00064"></a><span class="lineno"> 64</span>  <span class="keyword">virtual</span> ~<a class="code" href="classOpenMS_1_1DTAFile.html">DTAFile</a>();</div>
79
<div class="line"><a name="l00065"></a><span class="lineno"> 65</span> </div>
80
<div class="line"><a name="l00075"></a><span class="lineno"> 75</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> SpectrumType></div>
81
<div class="line"><a name="l00076"></a><span class="lineno"><a class="line" href="classOpenMS_1_1DTAFile.html#a583280bb0e47a5d57b337d6440c96b73"> 76</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1DTAFile.html#a583280bb0e47a5d57b337d6440c96b73">load</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & filename, SpectrumType & spectrum)</div>
82
<div class="line"><a name="l00077"></a><span class="lineno"> 77</span>  {</div>
83
<div class="line"><a name="l00078"></a><span class="lineno"> 78</span>  std::ifstream is(filename.c_str());</div>
84
<div class="line"><a name="l00079"></a><span class="lineno"> 79</span>  <span class="keywordflow">if</span> (!is)</div>
85
<div class="line"><a name="l00080"></a><span class="lineno"> 80</span>  {</div>
86
<div class="line"><a name="l00081"></a><span class="lineno"> 81</span>  <span class="keywordflow">throw</span> <a class="code" href="classOpenMS_1_1Exception_1_1FileNotFound.html">Exception::FileNotFound</a>(__FILE__, __LINE__, __PRETTY_FUNCTION__, filename);</div>
87
<div class="line"><a name="l00082"></a><span class="lineno"> 82</span>  }</div>
88
<div class="line"><a name="l00083"></a><span class="lineno"> 83</span> </div>
89
<div class="line"><a name="l00084"></a><span class="lineno"> 84</span>  <span class="comment">// Delete old spectrum</span></div>
90
<div class="line"><a name="l00085"></a><span class="lineno"> 85</span>  spectrum.clear(<span class="keyword">true</span>);</div>
91
<div class="line"><a name="l00086"></a><span class="lineno"> 86</span> </div>
92
<div class="line"><a name="l00087"></a><span class="lineno"> 87</span>  <span class="comment">//temporary variables</span></div>
93
<div class="line"><a name="l00088"></a><span class="lineno"> 88</span>  <a class="code" href="classOpenMS_1_1String.html">String</a> line;</div>
94
<div class="line"><a name="l00089"></a><span class="lineno"> 89</span>  std::vector<String> strings(2);</div>
95
<div class="line"><a name="l00090"></a><span class="lineno"> 90</span>  <span class="keyword">typename</span> <a class="code" href="namespaceOpenMS.html#a013338b7bdbb5c3b4c78666656070e23">SpectrumType::PeakType</a> p;</div>
96
<div class="line"><a name="l00091"></a><span class="lineno"> 91</span>  <span class="keywordtype">char</span> delimiter;</div>
97
<div class="line"><a name="l00092"></a><span class="lineno"> 92</span> </div>
98
<div class="line"><a name="l00093"></a><span class="lineno"> 93</span>  <span class="comment">// line number counter</span></div>
99
<div class="line"><a name="l00094"></a><span class="lineno"> 94</span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> line_number = 1;</div>
100
<div class="line"><a name="l00095"></a><span class="lineno"> 95</span> </div>
101
<div class="line"><a name="l00096"></a><span class="lineno"> 96</span>  <span class="comment">//read first line and store precursor m/z and charge</span></div>
102
<div class="line"><a name="l00097"></a><span class="lineno"> 97</span>  getline(is, line, <span class="charliteral">'\n'</span>);</div>
103
<div class="line"><a name="l00098"></a><span class="lineno"> 98</span>  line.<a class="code" href="classOpenMS_1_1String.html#a86864c88ee12eb322f1645f238c1dbe5">trim</a>();</div>
104
<div class="line"><a name="l00099"></a><span class="lineno"> 99</span> </div>
105
<div class="line"><a name="l00100"></a><span class="lineno"> 100</span>  <span class="comment">//test which delimiter is used in the line</span></div>
106
<div class="line"><a name="l00101"></a><span class="lineno"> 101</span>  <span class="keywordflow">if</span> (line.<a class="code" href="classOpenMS_1_1String.html#a58599d37159ebc08a654fb2d25be92fe">has</a>(<span class="charliteral">'\t'</span>))</div>
107
<div class="line"><a name="l00102"></a><span class="lineno"> 102</span>  {</div>
108
<div class="line"><a name="l00103"></a><span class="lineno"> 103</span>  delimiter = <span class="charliteral">'\t'</span>;</div>
109
<div class="line"><a name="l00104"></a><span class="lineno"> 104</span>  }</div>
110
<div class="line"><a name="l00105"></a><span class="lineno"> 105</span>  <span class="keywordflow">else</span></div>
111
<div class="line"><a name="l00106"></a><span class="lineno"> 106</span>  {</div>
112
<div class="line"><a name="l00107"></a><span class="lineno"> 107</span>  delimiter = <span class="charliteral">' '</span>;</div>
113
<div class="line"><a name="l00108"></a><span class="lineno"> 108</span>  }</div>
114
<div class="line"><a name="l00109"></a><span class="lineno"> 109</span> </div>
115
<div class="line"><a name="l00110"></a><span class="lineno"> 110</span>  line.<a class="code" href="classOpenMS_1_1String.html#ae580d960e12c7f0ebc5c95931cf39ad5">split</a>(delimiter, strings);</div>
116
<div class="line"><a name="l00111"></a><span class="lineno"> 111</span>  <span class="keywordflow">if</span> (strings.size() != 2)</div>
117
<div class="line"><a name="l00112"></a><span class="lineno"> 112</span>  {</div>
118
<div class="line"><a name="l00113"></a><span class="lineno"> 113</span>  <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">"Bad data line ("</span> + <a class="code" href="classOpenMS_1_1String.html">String</a>(line_number) + <span class="stringliteral">"): \""</span>) + line + <span class="stringliteral">"\" (got "</span> + <a class="code" href="classOpenMS_1_1String.html">String</a>(strings.size()) + <span class="stringliteral">", expected 2 entries)"</span>, filename);</div>
119
<div class="line"><a name="l00114"></a><span class="lineno"> 114</span>  }</div>
120
<div class="line"><a name="l00115"></a><span class="lineno"> 115</span>  <a class="code" href="classOpenMS_1_1Precursor.html">Precursor</a> precursor;</div>
121
<div class="line"><a name="l00116"></a><span class="lineno"> 116</span>  <a class="code" href="classdouble.html">DoubleReal</a> mh_mass;</div>
122
<div class="line"><a name="l00117"></a><span class="lineno"> 117</span>  <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> charge;</div>
123
<div class="line"><a name="l00118"></a><span class="lineno"> 118</span>  <span class="keywordflow">try</span></div>
124
<div class="line"><a name="l00119"></a><span class="lineno"> 119</span>  {</div>
125
<div class="line"><a name="l00120"></a><span class="lineno"> 120</span>  <span class="comment">// by convention the first line holds: singly protonated peptide mass, charge state</span></div>
126
<div class="line"><a name="l00121"></a><span class="lineno"> 121</span>  mh_mass = strings[0].toDouble();</div>
127
<div class="line"><a name="l00122"></a><span class="lineno"> 122</span>  charge = strings[1].toInt();</div>
128
<div class="line"><a name="l00123"></a><span class="lineno"> 123</span>  }</div>
129
<div class="line"><a name="l00124"></a><span class="lineno"> 124</span>  <span class="keywordflow">catch</span> (...)</div>
130
<div class="line"><a name="l00125"></a><span class="lineno"> 125</span>  {</div>
131
<div class="line"><a name="l00126"></a><span class="lineno"> 126</span>  <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">"Bad data line ("</span> + <a class="code" href="classOpenMS_1_1String.html">String</a>(line_number) + <span class="stringliteral">"): \""</span>) + line + <span class="stringliteral">"\": not a float number."</span>, filename);</div>
132
<div class="line"><a name="l00127"></a><span class="lineno"> 127</span>  }</div>
133
<div class="line"><a name="l00128"></a><span class="lineno"> 128</span>  <span class="keywordflow">if</span> (charge != 0)</div>
134
<div class="line"><a name="l00129"></a><span class="lineno"> 129</span>  {</div>
135
<div class="line"><a name="l00130"></a><span class="lineno"> 130</span>  precursor.<a class="code" href="classOpenMS_1_1Peak1D.html#ab9c4ce5d172a75d6de2c6f5f1847c9ab">setMZ</a>((mh_mass - <a class="code" href="namespaceOpenMS_1_1Constants.html#a7a25c5ed4c5f83b23ded7014aef42ad4">Constants::PROTON_MASS_U</a>) / charge + <a class="code" href="namespaceOpenMS_1_1Constants.html#a7a25c5ed4c5f83b23ded7014aef42ad4">Constants::PROTON_MASS_U</a>);</div>
136
<div class="line"><a name="l00131"></a><span class="lineno"> 131</span>  }</div>
137
<div class="line"><a name="l00132"></a><span class="lineno"> 132</span>  <span class="keywordflow">else</span></div>
138
<div class="line"><a name="l00133"></a><span class="lineno"> 133</span>  {</div>
139
<div class="line"><a name="l00134"></a><span class="lineno"> 134</span>  precursor.<a class="code" href="classOpenMS_1_1Peak1D.html#ab9c4ce5d172a75d6de2c6f5f1847c9ab">setMZ</a>(mh_mass);</div>
140
<div class="line"><a name="l00135"></a><span class="lineno"> 135</span>  }</div>
141
<div class="line"><a name="l00136"></a><span class="lineno"> 136</span>  precursor.<a class="code" href="classOpenMS_1_1Precursor.html#aca40a4630f5f8a0568899b74a62dcd4b">setCharge</a>(charge);</div>
142
<div class="line"><a name="l00137"></a><span class="lineno"> 137</span>  spectrum.getPrecursors().push_back(precursor);</div>
143
<div class="line"><a name="l00138"></a><span class="lineno"> 138</span> </div>
144
<div class="line"><a name="l00139"></a><span class="lineno"> 139</span>  <span class="keywordflow">while</span> (getline(is, line, <span class="charliteral">'\n'</span>))</div>
145
<div class="line"><a name="l00140"></a><span class="lineno"> 140</span>  {</div>
146
<div class="line"><a name="l00141"></a><span class="lineno"> 141</span>  ++line_number;</div>
147
<div class="line"><a name="l00142"></a><span class="lineno"> 142</span>  line.<a class="code" href="classOpenMS_1_1String.html#a86864c88ee12eb322f1645f238c1dbe5">trim</a>();</div>
148
<div class="line"><a name="l00143"></a><span class="lineno"> 143</span>  <span class="keywordflow">if</span> (line.empty()) <span class="keywordflow">continue</span>;</div>
149
<div class="line"><a name="l00144"></a><span class="lineno"> 144</span> </div>
150
<div class="line"><a name="l00145"></a><span class="lineno"> 145</span>  <span class="comment">//test which delimiter is used in the line</span></div>
151
<div class="line"><a name="l00146"></a><span class="lineno"> 146</span>  <span class="keywordflow">if</span> (line.<a class="code" href="classOpenMS_1_1String.html#a58599d37159ebc08a654fb2d25be92fe">has</a>(<span class="charliteral">'\t'</span>))</div>
152
<div class="line"><a name="l00147"></a><span class="lineno"> 147</span>  {</div>
153
<div class="line"><a name="l00148"></a><span class="lineno"> 148</span>  delimiter = <span class="charliteral">'\t'</span>;</div>
154
<div class="line"><a name="l00149"></a><span class="lineno"> 149</span>  }</div>
155
<div class="line"><a name="l00150"></a><span class="lineno"> 150</span>  <span class="keywordflow">else</span></div>
156
<div class="line"><a name="l00151"></a><span class="lineno"> 151</span>  {</div>
157
<div class="line"><a name="l00152"></a><span class="lineno"> 152</span>  delimiter = <span class="charliteral">' '</span>;</div>
158
<div class="line"><a name="l00153"></a><span class="lineno"> 153</span>  }</div>
159
<div class="line"><a name="l00154"></a><span class="lineno"> 154</span> </div>
160
<div class="line"><a name="l00155"></a><span class="lineno"> 155</span>  line.<a class="code" href="classOpenMS_1_1String.html#ae580d960e12c7f0ebc5c95931cf39ad5">split</a>(delimiter, strings);</div>
161
<div class="line"><a name="l00156"></a><span class="lineno"> 156</span>  <span class="keywordflow">if</span> (strings.size() != 2)</div>
162
<div class="line"><a name="l00157"></a><span class="lineno"> 157</span>  {</div>
163
<div class="line"><a name="l00158"></a><span class="lineno"> 158</span>  <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">"Bad data line ("</span> + <a class="code" href="classOpenMS_1_1String.html">String</a>(line_number) + <span class="stringliteral">"): \""</span>) + line + <span class="stringliteral">"\" (got "</span> + <a class="code" href="classOpenMS_1_1String.html">String</a>(strings.size()) + <span class="stringliteral">", expected 2 entries)"</span>, filename);</div>
164
<div class="line"><a name="l00159"></a><span class="lineno"> 159</span>  }</div>
165
<div class="line"><a name="l00160"></a><span class="lineno"> 160</span>  <span class="keywordflow">try</span></div>
166
<div class="line"><a name="l00161"></a><span class="lineno"> 161</span>  {</div>
167
<div class="line"><a name="l00162"></a><span class="lineno"> 162</span>  <span class="comment">//fill peak</span></div>
168
<div class="line"><a name="l00163"></a><span class="lineno"> 163</span>  p.setPosition((<span class="keyword">typename</span> SpectrumType::PeakType::PositionType)strings[0].toDouble());</div>
169
<div class="line"><a name="l00164"></a><span class="lineno"> 164</span>  p.setIntensity((<span class="keyword">typename</span> SpectrumType::PeakType::IntensityType)strings[1].toDouble());</div>
170
<div class="line"><a name="l00165"></a><span class="lineno"> 165</span>  }</div>
171
<div class="line"><a name="l00166"></a><span class="lineno"> 166</span>  <span class="keywordflow">catch</span> (<a class="code" href="classOpenMS_1_1Exception_1_1BaseException.html">Exception::BaseException</a> & <span class="comment">/*e*/</span>)</div>
172
<div class="line"><a name="l00167"></a><span class="lineno"> 167</span>  {</div>
173
<div class="line"><a name="l00168"></a><span class="lineno"> 168</span>  <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">"Bad data line ("</span> + <a class="code" href="classOpenMS_1_1String.html">String</a>(line_number) + <span class="stringliteral">"): \""</span>) + line + <span class="stringliteral">"\": not a float number."</span>, filename);</div>
174
<div class="line"><a name="l00169"></a><span class="lineno"> 169</span>  }</div>
175
<div class="line"><a name="l00170"></a><span class="lineno"> 170</span>  spectrum.push_back(p);</div>
176
<div class="line"><a name="l00171"></a><span class="lineno"> 171</span>  }</div>
177
<div class="line"><a name="l00172"></a><span class="lineno"> 172</span> </div>
178
<div class="line"><a name="l00173"></a><span class="lineno"> 173</span>  spectrum.setName(<a class="code" href="classOpenMS_1_1File.html#a6487771c96fec9db032960c91864884e">File::basename</a>(filename));</div>
179
<div class="line"><a name="l00174"></a><span class="lineno"> 174</span>  is.close();</div>
180
<div class="line"><a name="l00175"></a><span class="lineno"> 175</span>  }</div>
181
<div class="line"><a name="l00176"></a><span class="lineno"> 176</span> </div>
182
<div class="line"><a name="l00185"></a><span class="lineno"> 185</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> SpectrumType></div>
183
<div class="line"><a name="l00186"></a><span class="lineno"><a class="line" href="classOpenMS_1_1DTAFile.html#aad1400476baaa9e6ff74301f6395c5e8"> 186</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1DTAFile.html#aad1400476baaa9e6ff74301f6395c5e8">store</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & filename, <span class="keyword">const</span> SpectrumType & spectrum)<span class="keyword"> const</span></div>
184
<div class="line"><a name="l00187"></a><span class="lineno"> 187</span> <span class="keyword"> </span>{</div>
185
<div class="line"><a name="l00188"></a><span class="lineno"> 188</span>  std::ofstream os(filename.c_str());</div>
186
<div class="line"><a name="l00189"></a><span class="lineno"> 189</span>  <span class="keywordflow">if</span> (!os)</div>
187
<div class="line"><a name="l00190"></a><span class="lineno"> 190</span>  {</div>
188
<div class="line"><a name="l00191"></a><span class="lineno"> 191</span>  <span class="keywordflow">throw</span> <a class="code" href="classOpenMS_1_1Exception_1_1UnableToCreateFile.html">Exception::UnableToCreateFile</a>(__FILE__, __LINE__, __PRETTY_FUNCTION__, filename);</div>
189
<div class="line"><a name="l00192"></a><span class="lineno"> 192</span>  }</div>
190
<div class="line"><a name="l00193"></a><span class="lineno"> 193</span>  os.precision(writtenDigits<DoubleReal>());</div>
191
<div class="line"><a name="l00194"></a><span class="lineno"> 194</span> </div>
192
<div class="line"><a name="l00195"></a><span class="lineno"> 195</span>  <span class="comment">//write precursor information</span></div>
193
<div class="line"><a name="l00196"></a><span class="lineno"> 196</span>  <a class="code" href="classOpenMS_1_1Precursor.html">Precursor</a> precursor;</div>
194
<div class="line"><a name="l00197"></a><span class="lineno"> 197</span>  <span class="keywordflow">if</span> (spectrum.getPrecursors().size() > 0)</div>
195
<div class="line"><a name="l00198"></a><span class="lineno"> 198</span>  {</div>
196
<div class="line"><a name="l00199"></a><span class="lineno"> 199</span>  precursor = spectrum.getPrecursors()[0];</div>
197
<div class="line"><a name="l00200"></a><span class="lineno"> 200</span>  }</div>
198
<div class="line"><a name="l00201"></a><span class="lineno"> 201</span>  <span class="keywordflow">if</span> (spectrum.getPrecursors().size() > 1)</div>
199
<div class="line"><a name="l00202"></a><span class="lineno"> 202</span>  {</div>
200
<div class="line"><a name="l00203"></a><span class="lineno"> 203</span>  std::cerr << <span class="stringliteral">"Warning: The spectrum written to the DTA file '"</span> << filename << <span class="stringliteral">"' has more than one precursor. The first precursor is used!"</span> << <span class="stringliteral">"\n"</span>;</div>
201
<div class="line"><a name="l00204"></a><span class="lineno"> 204</span>  }</div>
202
<div class="line"><a name="l00205"></a><span class="lineno"> 205</span>  <span class="comment">//unknown charge</span></div>
203
<div class="line"><a name="l00206"></a><span class="lineno"> 206</span>  <span class="keywordflow">if</span> (precursor.<a class="code" href="classOpenMS_1_1Precursor.html#ab91109da6782d902c745c771aa85d03d">getCharge</a>() == 0)</div>
204
<div class="line"><a name="l00207"></a><span class="lineno"> 207</span>  {</div>
205
<div class="line"><a name="l00208"></a><span class="lineno"> 208</span>  os << precursor.<a class="code" href="classOpenMS_1_1Peak1D.html#a6fefef82aae7a3208e71648e763d5ea4">getMZ</a>();</div>
206
<div class="line"><a name="l00209"></a><span class="lineno"> 209</span>  }</div>
207
<div class="line"><a name="l00210"></a><span class="lineno"> 210</span>  <span class="comment">//known charge</span></div>
208
<div class="line"><a name="l00211"></a><span class="lineno"> 211</span>  <span class="keywordflow">else</span></div>
209
<div class="line"><a name="l00212"></a><span class="lineno"> 212</span>  {</div>
210
<div class="line"><a name="l00213"></a><span class="lineno"> 213</span>  os << ((precursor.<a class="code" href="classOpenMS_1_1Peak1D.html#a6fefef82aae7a3208e71648e763d5ea4">getMZ</a>() - 1.0) * precursor.<a class="code" href="classOpenMS_1_1Precursor.html#ab91109da6782d902c745c771aa85d03d">getCharge</a>() + 1.0);</div>
211
<div class="line"><a name="l00214"></a><span class="lineno"> 214</span>  }</div>
212
<div class="line"><a name="l00215"></a><span class="lineno"> 215</span>  <span class="comment">//charge</span></div>
213
<div class="line"><a name="l00216"></a><span class="lineno"> 216</span>  os << <span class="stringliteral">" "</span> << precursor.<a class="code" href="classOpenMS_1_1Precursor.html#ab91109da6782d902c745c771aa85d03d">getCharge</a>() << <span class="stringliteral">"\n"</span>;</div>
214
<div class="line"><a name="l00217"></a><span class="lineno"> 217</span> </div>
215
<div class="line"><a name="l00218"></a><span class="lineno"> 218</span>  <span class="comment">// Iterate over all peaks of the spectrum and</span></div>
216
<div class="line"><a name="l00219"></a><span class="lineno"> 219</span>  <span class="comment">// write one line for each peak of the spectrum.</span></div>
217
<div class="line"><a name="l00220"></a><span class="lineno"> 220</span>  <span class="keyword">typename</span> SpectrumType::ConstIterator it(spectrum.begin());</div>
218
<div class="line"><a name="l00221"></a><span class="lineno"> 221</span>  <span class="keywordflow">for</span> (; it != spectrum.end(); ++it)</div>
219
<div class="line"><a name="l00222"></a><span class="lineno"> 222</span>  {</div>
220
<div class="line"><a name="l00223"></a><span class="lineno"> 223</span>  <span class="comment">// Write m/z and intensity.</span></div>
221
<div class="line"><a name="l00224"></a><span class="lineno"> 224</span>  os << it->getPosition() << <span class="stringliteral">" "</span> << it->getIntensity() << <span class="stringliteral">"\n"</span>;</div>
222
<div class="line"><a name="l00225"></a><span class="lineno"> 225</span>  }</div>
223
<div class="line"><a name="l00226"></a><span class="lineno"> 226</span> </div>
224
<div class="line"><a name="l00227"></a><span class="lineno"> 227</span>  <span class="comment">// Done.</span></div>
225
<div class="line"><a name="l00228"></a><span class="lineno"> 228</span>  os.close();</div>
226
<div class="line"><a name="l00229"></a><span class="lineno"> 229</span>  }</div>
227
<div class="line"><a name="l00230"></a><span class="lineno"> 230</span> </div>
228
<div class="line"><a name="l00231"></a><span class="lineno"> 231</span>  };</div>
229
<div class="line"><a name="l00232"></a><span class="lineno"> 232</span> } <span class="comment">// namespace OpenMS</span></div>
230
<div class="line"><a name="l00233"></a><span class="lineno"> 233</span> </div>
231
<div class="line"><a name="l00234"></a><span class="lineno"> 234</span> <span class="preprocessor">#endif // OPENMS_FORMAT_DTAFILE_H</span></div>
232
<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>
233
<div class="ttc" id="classOpenMS_1_1Precursor_html"><div class="ttname"><a href="classOpenMS_1_1Precursor.html">OpenMS::Precursor</a></div><div class="ttdoc">Precursor meta information. </div><div class="ttdef"><b>Definition:</b> Precursor.h:56</div></div>
234
<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>
235
<div class="ttc" id="classOpenMS_1_1Peak1D_html_a6fefef82aae7a3208e71648e763d5ea4"><div class="ttname"><a href="classOpenMS_1_1Peak1D.html#a6fefef82aae7a3208e71648e763d5ea4">OpenMS::Peak1D::getMZ</a></div><div class="ttdeci">CoordinateType getMZ() const </div><div class="ttdoc">Non-mutable access to m/z. </div><div class="ttdef"><b>Definition:</b> Peak1D.h:108</div></div>
236
<div class="ttc" id="classOpenMS_1_1DTAFile_html"><div class="ttname"><a href="classOpenMS_1_1DTAFile.html">OpenMS::DTAFile</a></div><div class="ttdoc">File adapter for DTA files. </div><div class="ttdef"><b>Definition:</b> DTAFile.h:58</div></div>
237
<div class="ttc" id="classOpenMS_1_1Precursor_html_ab91109da6782d902c745c771aa85d03d"><div class="ttname"><a href="classOpenMS_1_1Precursor.html#ab91109da6782d902c745c771aa85d03d">OpenMS::Precursor::getCharge</a></div><div class="ttdeci">Int getCharge() const </div><div class="ttdoc">Non-mutable access to the charge. </div></div>
238
<div class="ttc" id="classdouble_html"><div class="ttname"><a href="classdouble.html">double</a></div></div>
239
<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>
240
<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>
241
<div class="ttc" id="classOpenMS_1_1Peak1D_html_ab9c4ce5d172a75d6de2c6f5f1847c9ab"><div class="ttname"><a href="classOpenMS_1_1Peak1D.html#ab9c4ce5d172a75d6de2c6f5f1847c9ab">OpenMS::Peak1D::setMZ</a></div><div class="ttdeci">void setMZ(CoordinateType mz)</div><div class="ttdoc">Mutable access to m/z. </div><div class="ttdef"><b>Definition:</b> Peak1D.h:114</div></div>
242
<div class="ttc" id="namespaceOpenMS_1_1Constants_html_a7a25c5ed4c5f83b23ded7014aef42ad4"><div class="ttname"><a href="namespaceOpenMS_1_1Constants.html#a7a25c5ed4c5f83b23ded7014aef42ad4">OpenMS::Constants::PROTON_MASS_U</a></div><div class="ttdeci">const double PROTON_MASS_U</div></div>
243
<div class="ttc" id="File_8h_html"><div class="ttname"><a href="File_8h.html">File.h</a></div></div>
244
<div class="ttc" id="classOpenMS_1_1DTAFile_html_a583280bb0e47a5d57b337d6440c96b73"><div class="ttname"><a href="classOpenMS_1_1DTAFile.html#a583280bb0e47a5d57b337d6440c96b73">OpenMS::DTAFile::load</a></div><div class="ttdeci">void load(const String &filename, SpectrumType &spectrum)</div><div class="ttdoc">Loads a DTA file to a spectrum. </div><div class="ttdef"><b>Definition:</b> DTAFile.h:76</div></div>
245
<div class="ttc" id="Constants_8h_html"><div class="ttname"><a href="Constants_8h.html">Constants.h</a></div></div>
246
<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 & trim()</div><div class="ttdoc">removes whitespaces (space, tab, line feed, carriage return) at the beginning and the end of the stri...</div></div>
247
<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>
248
<div class="ttc" id="classOpenMS_1_1File_html_a6487771c96fec9db032960c91864884e"><div class="ttname"><a href="classOpenMS_1_1File.html#a6487771c96fec9db032960c91864884e">OpenMS::File::basename</a></div><div class="ttdeci">static String basename(const String &file)</div><div class="ttdoc">Returns the basename of the file (without the path). </div></div>
249
<div class="ttc" id="classOpenMS_1_1DTAFile_html_aad1400476baaa9e6ff74301f6395c5e8"><div class="ttname"><a href="classOpenMS_1_1DTAFile.html#aad1400476baaa9e6ff74301f6395c5e8">OpenMS::DTAFile::store</a></div><div class="ttdeci">void store(const String &filename, const SpectrumType &spectrum) const </div><div class="ttdoc">Stores a spectrum in a DTA file. </div><div class="ttdef"><b>Definition:</b> DTAFile.h:186</div></div>
250
<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>
251
<div class="ttc" id="Precursor_8h_html"><div class="ttname"><a href="Precursor_8h.html">Precursor.h</a></div></div>
252
<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>
253
<div class="ttc" id="classOpenMS_1_1Precursor_html_aca40a4630f5f8a0568899b74a62dcd4b"><div class="ttname"><a href="classOpenMS_1_1Precursor.html#aca40a4630f5f8a0568899b74a62dcd4b">OpenMS::Precursor::setCharge</a></div><div class="ttdeci">void setCharge(Int charge)</div><div class="ttdoc">Mutable access to the charge. </div></div>
254
<div class="ttc" id="group__Concept_html_ga7cc214a236ad3bb6ad435bdcf5262a3f"><div class="ttname"><a href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">OpenMS::Int</a></div><div class="ttdeci">int Int</div><div class="ttdoc">Signed integer type. </div><div class="ttdef"><b>Definition:</b> Types.h:100</div></div>
255
<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< String > &substrings, bool quote_protect=false) const </div><div class="ttdoc">Splits a string into substrings using splitter as delimiter. </div></div>
256
<div class="ttc" id="String_8h_html"><div class="ttname"><a href="String_8h.html">String.h</a></div></div>
257
<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>
258
</div><!-- fragment --></div><!-- contents -->
259
<HR style="height:1px; border:none; border-top:1px solid #c0c0c0;">
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<TABLE width="100%" border="0">
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<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
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<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:13 using doxygen 1.8.5</font></TD>
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