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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>&#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>
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<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_DTAFILE_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_DTAFILE_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="Constants_8h.html">OpenMS/CONCEPT/Constants.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="Precursor_8h.html">OpenMS/METADATA/Precursor.h</a>&gt;</span></div>
<div class="line"><a name="l00041"></a><span class="lineno">   41</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="File_8h.html">OpenMS/SYSTEM/File.h</a>&gt;</span></div>
<div class="line"><a name="l00042"></a><span class="lineno">   42</span>&#160;</div>
<div class="line"><a name="l00043"></a><span class="lineno">   43</span>&#160;<span class="preprocessor">#include &lt;fstream&gt;</span></div>
<div class="line"><a name="l00044"></a><span class="lineno">   44</span>&#160;<span class="preprocessor">#include &lt;vector&gt;</span></div>
<div class="line"><a name="l00045"></a><span class="lineno">   45</span>&#160;</div>
<div class="line"><a name="l00046"></a><span class="lineno">   46</span>&#160;<span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00047"></a><span class="lineno">   47</span>&#160;{</div>
<div class="line"><a name="l00058"></a><span class="lineno"><a class="line" href="classOpenMS_1_1DTAFile.html">   58</a></span>&#160;  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1DTAFile.html">DTAFile</a></div>
<div class="line"><a name="l00059"></a><span class="lineno">   59</span>&#160;  {</div>
<div class="line"><a name="l00060"></a><span class="lineno">   60</span>&#160;<span class="keyword">public</span>:</div>
<div class="line"><a name="l00062"></a><span class="lineno">   62</span>&#160;    <a class="code" href="classOpenMS_1_1DTAFile.html">DTAFile</a>();</div>
<div class="line"><a name="l00064"></a><span class="lineno">   64</span>&#160;    <span class="keyword">virtual</span> ~<a class="code" href="classOpenMS_1_1DTAFile.html">DTAFile</a>();</div>
<div class="line"><a name="l00065"></a><span class="lineno">   65</span>&#160;</div>
<div class="line"><a name="l00075"></a><span class="lineno">   75</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">typename</span> SpectrumType&gt;</div>
<div class="line"><a name="l00076"></a><span class="lineno"><a class="line" href="classOpenMS_1_1DTAFile.html#a583280bb0e47a5d57b337d6440c96b73">   76</a></span>&#160;    <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> &amp; filename, SpectrumType &amp; spectrum)</div>
<div class="line"><a name="l00077"></a><span class="lineno">   77</span>&#160;    {</div>
<div class="line"><a name="l00078"></a><span class="lineno">   78</span>&#160;      std::ifstream is(filename.c_str());</div>
<div class="line"><a name="l00079"></a><span class="lineno">   79</span>&#160;      <span class="keywordflow">if</span> (!is)</div>
<div class="line"><a name="l00080"></a><span class="lineno">   80</span>&#160;      {</div>
<div class="line"><a name="l00081"></a><span class="lineno">   81</span>&#160;        <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="l00082"></a><span class="lineno">   82</span>&#160;      }</div>
<div class="line"><a name="l00083"></a><span class="lineno">   83</span>&#160;</div>
<div class="line"><a name="l00084"></a><span class="lineno">   84</span>&#160;      <span class="comment">//  Delete old spectrum</span></div>
<div class="line"><a name="l00085"></a><span class="lineno">   85</span>&#160;      spectrum.clear(<span class="keyword">true</span>);</div>
<div class="line"><a name="l00086"></a><span class="lineno">   86</span>&#160;</div>
<div class="line"><a name="l00087"></a><span class="lineno">   87</span>&#160;      <span class="comment">//temporary variables</span></div>
<div class="line"><a name="l00088"></a><span class="lineno">   88</span>&#160;      <a class="code" href="classOpenMS_1_1String.html">String</a> line;</div>
<div class="line"><a name="l00089"></a><span class="lineno">   89</span>&#160;      std::vector&lt;String&gt; strings(2);</div>
<div class="line"><a name="l00090"></a><span class="lineno">   90</span>&#160;      <span class="keyword">typename</span> <a class="code" href="namespaceOpenMS.html#a013338b7bdbb5c3b4c78666656070e23">SpectrumType::PeakType</a> p;</div>
<div class="line"><a name="l00091"></a><span class="lineno">   91</span>&#160;      <span class="keywordtype">char</span> delimiter;</div>
<div class="line"><a name="l00092"></a><span class="lineno">   92</span>&#160;</div>
<div class="line"><a name="l00093"></a><span class="lineno">   93</span>&#160;      <span class="comment">// line number counter</span></div>
<div class="line"><a name="l00094"></a><span class="lineno">   94</span>&#160;      <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> line_number = 1;</div>
<div class="line"><a name="l00095"></a><span class="lineno">   95</span>&#160;</div>
<div class="line"><a name="l00096"></a><span class="lineno">   96</span>&#160;      <span class="comment">//read first line and store precursor m/z and charge</span></div>
<div class="line"><a name="l00097"></a><span class="lineno">   97</span>&#160;      getline(is, line, <span class="charliteral">&#39;\n&#39;</span>);</div>
<div class="line"><a name="l00098"></a><span class="lineno">   98</span>&#160;      line.<a class="code" href="classOpenMS_1_1String.html#a86864c88ee12eb322f1645f238c1dbe5">trim</a>();</div>
<div class="line"><a name="l00099"></a><span class="lineno">   99</span>&#160;</div>
<div class="line"><a name="l00100"></a><span class="lineno">  100</span>&#160;      <span class="comment">//test which delimiter is used in the line</span></div>
<div class="line"><a name="l00101"></a><span class="lineno">  101</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="l00102"></a><span class="lineno">  102</span>&#160;      {</div>
<div class="line"><a name="l00103"></a><span class="lineno">  103</span>&#160;        delimiter = <span class="charliteral">&#39;\t&#39;</span>;</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;      <span class="keywordflow">else</span></div>
<div class="line"><a name="l00106"></a><span class="lineno">  106</span>&#160;      {</div>
<div class="line"><a name="l00107"></a><span class="lineno">  107</span>&#160;        delimiter = <span class="charliteral">&#39; &#39;</span>;</div>
<div class="line"><a name="l00108"></a><span class="lineno">  108</span>&#160;      }</div>
<div class="line"><a name="l00109"></a><span class="lineno">  109</span>&#160;</div>
<div class="line"><a name="l00110"></a><span class="lineno">  110</span>&#160;      line.<a class="code" href="classOpenMS_1_1String.html#ae580d960e12c7f0ebc5c95931cf39ad5">split</a>(delimiter, strings);</div>
<div class="line"><a name="l00111"></a><span class="lineno">  111</span>&#160;      <span class="keywordflow">if</span> (strings.size() != 2)</div>
<div class="line"><a name="l00112"></a><span class="lineno">  112</span>&#160;      {</div>
<div class="line"><a name="l00113"></a><span class="lineno">  113</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 2 entries)&quot;</span>, filename);</div>
<div class="line"><a name="l00114"></a><span class="lineno">  114</span>&#160;      }</div>
<div class="line"><a name="l00115"></a><span class="lineno">  115</span>&#160;      <a class="code" href="classOpenMS_1_1Precursor.html">Precursor</a> precursor;</div>
<div class="line"><a name="l00116"></a><span class="lineno">  116</span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> mh_mass;</div>
<div class="line"><a name="l00117"></a><span class="lineno">  117</span>&#160;      <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> charge;</div>
<div class="line"><a name="l00118"></a><span class="lineno">  118</span>&#160;      <span class="keywordflow">try</span></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">// by convention the first line holds: singly protonated peptide mass, charge state</span></div>
<div class="line"><a name="l00121"></a><span class="lineno">  121</span>&#160;        mh_mass = strings[0].toDouble();</div>
<div class="line"><a name="l00122"></a><span class="lineno">  122</span>&#160;        charge = strings[1].toInt();</div>
<div class="line"><a name="l00123"></a><span class="lineno">  123</span>&#160;      }</div>
<div class="line"><a name="l00124"></a><span class="lineno">  124</span>&#160;      <span class="keywordflow">catch</span> (...)</div>
<div class="line"><a name="l00125"></a><span class="lineno">  125</span>&#160;      {</div>
<div class="line"><a name="l00126"></a><span class="lineno">  126</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;: not a float number.&quot;</span>, filename);</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="keywordflow">if</span> (charge != 0)</div>
<div class="line"><a name="l00129"></a><span class="lineno">  129</span>&#160;      {</div>
<div class="line"><a name="l00130"></a><span class="lineno">  130</span>&#160;        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>
<div class="line"><a name="l00131"></a><span class="lineno">  131</span>&#160;      }</div>
<div class="line"><a name="l00132"></a><span class="lineno">  132</span>&#160;      <span class="keywordflow">else</span></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;        precursor.<a class="code" href="classOpenMS_1_1Peak1D.html#ab9c4ce5d172a75d6de2c6f5f1847c9ab">setMZ</a>(mh_mass);</div>
<div class="line"><a name="l00135"></a><span class="lineno">  135</span>&#160;      }</div>
<div class="line"><a name="l00136"></a><span class="lineno">  136</span>&#160;      precursor.<a class="code" href="classOpenMS_1_1Precursor.html#aca40a4630f5f8a0568899b74a62dcd4b">setCharge</a>(charge);</div>
<div class="line"><a name="l00137"></a><span class="lineno">  137</span>&#160;      spectrum.getPrecursors().push_back(precursor);</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;      <span class="keywordflow">while</span> (getline(is, line, <span class="charliteral">&#39;\n&#39;</span>))</div>
<div class="line"><a name="l00140"></a><span class="lineno">  140</span>&#160;      {</div>
<div class="line"><a name="l00141"></a><span class="lineno">  141</span>&#160;        ++line_number;</div>
<div class="line"><a name="l00142"></a><span class="lineno">  142</span>&#160;        line.<a class="code" href="classOpenMS_1_1String.html#a86864c88ee12eb322f1645f238c1dbe5">trim</a>();</div>
<div class="line"><a name="l00143"></a><span class="lineno">  143</span>&#160;        <span class="keywordflow">if</span> (line.empty()) <span class="keywordflow">continue</span>;</div>
<div class="line"><a name="l00144"></a><span class="lineno">  144</span>&#160;</div>
<div class="line"><a name="l00145"></a><span class="lineno">  145</span>&#160;        <span class="comment">//test which delimiter is used in the line</span></div>
<div class="line"><a name="l00146"></a><span class="lineno">  146</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="l00147"></a><span class="lineno">  147</span>&#160;        {</div>
<div class="line"><a name="l00148"></a><span class="lineno">  148</span>&#160;          delimiter = <span class="charliteral">&#39;\t&#39;</span>;</div>
<div class="line"><a name="l00149"></a><span class="lineno">  149</span>&#160;        }</div>
<div class="line"><a name="l00150"></a><span class="lineno">  150</span>&#160;        <span class="keywordflow">else</span></div>
<div class="line"><a name="l00151"></a><span class="lineno">  151</span>&#160;        {</div>
<div class="line"><a name="l00152"></a><span class="lineno">  152</span>&#160;          delimiter = <span class="charliteral">&#39; &#39;</span>;</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;</div>
<div class="line"><a name="l00155"></a><span class="lineno">  155</span>&#160;        line.<a class="code" href="classOpenMS_1_1String.html#ae580d960e12c7f0ebc5c95931cf39ad5">split</a>(delimiter, strings);</div>
<div class="line"><a name="l00156"></a><span class="lineno">  156</span>&#160;        <span class="keywordflow">if</span> (strings.size() != 2)</div>
<div class="line"><a name="l00157"></a><span class="lineno">  157</span>&#160;        {</div>
<div class="line"><a name="l00158"></a><span class="lineno">  158</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 2 entries)&quot;</span>, filename);</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="keywordflow">try</span></div>
<div class="line"><a name="l00161"></a><span class="lineno">  161</span>&#160;        {</div>
<div class="line"><a name="l00162"></a><span class="lineno">  162</span>&#160;          <span class="comment">//fill peak</span></div>
<div class="line"><a name="l00163"></a><span class="lineno">  163</span>&#160;          p.setPosition((<span class="keyword">typename</span> SpectrumType::PeakType::PositionType)strings[0].toDouble());</div>
<div class="line"><a name="l00164"></a><span class="lineno">  164</span>&#160;          p.setIntensity((<span class="keyword">typename</span> SpectrumType::PeakType::IntensityType)strings[1].toDouble());</div>
<div class="line"><a name="l00165"></a><span class="lineno">  165</span>&#160;        }</div>
<div class="line"><a name="l00166"></a><span class="lineno">  166</span>&#160;        <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="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">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;: not a float number.&quot;</span>, filename);</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;        spectrum.push_back(p);</div>
<div class="line"><a name="l00171"></a><span class="lineno">  171</span>&#160;      }</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;      spectrum.setName(<a class="code" href="classOpenMS_1_1File.html#a6487771c96fec9db032960c91864884e">File::basename</a>(filename));</div>
<div class="line"><a name="l00174"></a><span class="lineno">  174</span>&#160;      is.close();</div>
<div class="line"><a name="l00175"></a><span class="lineno">  175</span>&#160;    }</div>
<div class="line"><a name="l00176"></a><span class="lineno">  176</span>&#160;</div>
<div class="line"><a name="l00185"></a><span class="lineno">  185</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">typename</span> SpectrumType&gt;</div>
<div class="line"><a name="l00186"></a><span class="lineno"><a class="line" href="classOpenMS_1_1DTAFile.html#aad1400476baaa9e6ff74301f6395c5e8">  186</a></span>&#160;    <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> &amp; filename, <span class="keyword">const</span> SpectrumType &amp; spectrum)<span class="keyword"> const</span></div>
<div class="line"><a name="l00187"></a><span class="lineno">  187</span>&#160;<span class="keyword">    </span>{</div>
<div class="line"><a name="l00188"></a><span class="lineno">  188</span>&#160;      std::ofstream os(filename.c_str());</div>
<div class="line"><a name="l00189"></a><span class="lineno">  189</span>&#160;      <span class="keywordflow">if</span> (!os)</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;        <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="l00192"></a><span class="lineno">  192</span>&#160;      }</div>
<div class="line"><a name="l00193"></a><span class="lineno">  193</span>&#160;      os.precision(writtenDigits&lt;DoubleReal&gt;());</div>
<div class="line"><a name="l00194"></a><span class="lineno">  194</span>&#160;</div>
<div class="line"><a name="l00195"></a><span class="lineno">  195</span>&#160;      <span class="comment">//write precursor information</span></div>
<div class="line"><a name="l00196"></a><span class="lineno">  196</span>&#160;      <a class="code" href="classOpenMS_1_1Precursor.html">Precursor</a> precursor;</div>
<div class="line"><a name="l00197"></a><span class="lineno">  197</span>&#160;      <span class="keywordflow">if</span> (spectrum.getPrecursors().size() &gt; 0)</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;        precursor = spectrum.getPrecursors()[0];</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;      <span class="keywordflow">if</span> (spectrum.getPrecursors().size() &gt; 1)</div>
<div class="line"><a name="l00202"></a><span class="lineno">  202</span>&#160;      {</div>
<div class="line"><a name="l00203"></a><span class="lineno">  203</span>&#160;        std::cerr &lt;&lt; <span class="stringliteral">&quot;Warning: The spectrum written to the DTA file &#39;&quot;</span> &lt;&lt; filename &lt;&lt; <span class="stringliteral">&quot;&#39; has more than one precursor. The first precursor is used!&quot;</span> &lt;&lt; <span class="stringliteral">&quot;\n&quot;</span>;</div>
<div class="line"><a name="l00204"></a><span class="lineno">  204</span>&#160;      }</div>
<div class="line"><a name="l00205"></a><span class="lineno">  205</span>&#160;      <span class="comment">//unknown charge</span></div>
<div class="line"><a name="l00206"></a><span class="lineno">  206</span>&#160;      <span class="keywordflow">if</span> (precursor.<a class="code" href="classOpenMS_1_1Precursor.html#ab91109da6782d902c745c771aa85d03d">getCharge</a>() == 0)</div>
<div class="line"><a name="l00207"></a><span class="lineno">  207</span>&#160;      {</div>
<div class="line"><a name="l00208"></a><span class="lineno">  208</span>&#160;        os &lt;&lt; precursor.<a class="code" href="classOpenMS_1_1Peak1D.html#a6fefef82aae7a3208e71648e763d5ea4">getMZ</a>();</div>
<div class="line"><a name="l00209"></a><span class="lineno">  209</span>&#160;      }</div>
<div class="line"><a name="l00210"></a><span class="lineno">  210</span>&#160;      <span class="comment">//known charge</span></div>
<div class="line"><a name="l00211"></a><span class="lineno">  211</span>&#160;      <span class="keywordflow">else</span></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;        os &lt;&lt; ((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>
<div class="line"><a name="l00214"></a><span class="lineno">  214</span>&#160;      }</div>
<div class="line"><a name="l00215"></a><span class="lineno">  215</span>&#160;      <span class="comment">//charge</span></div>
<div class="line"><a name="l00216"></a><span class="lineno">  216</span>&#160;      os &lt;&lt; <span class="stringliteral">&quot; &quot;</span> &lt;&lt; precursor.<a class="code" href="classOpenMS_1_1Precursor.html#ab91109da6782d902c745c771aa85d03d">getCharge</a>() &lt;&lt; <span class="stringliteral">&quot;\n&quot;</span>;</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;      <span class="comment">// Iterate over all peaks of the spectrum and</span></div>
<div class="line"><a name="l00219"></a><span class="lineno">  219</span>&#160;      <span class="comment">// write one line for each peak of the spectrum.</span></div>
<div class="line"><a name="l00220"></a><span class="lineno">  220</span>&#160;      <span class="keyword">typename</span> SpectrumType::ConstIterator it(spectrum.begin());</div>
<div class="line"><a name="l00221"></a><span class="lineno">  221</span>&#160;      <span class="keywordflow">for</span> (; it != spectrum.end(); ++it)</div>
<div class="line"><a name="l00222"></a><span class="lineno">  222</span>&#160;      {</div>
<div class="line"><a name="l00223"></a><span class="lineno">  223</span>&#160;        <span class="comment">// Write m/z and intensity.</span></div>
<div class="line"><a name="l00224"></a><span class="lineno">  224</span>&#160;        os &lt;&lt; it-&gt;getPosition() &lt;&lt; <span class="stringliteral">&quot; &quot;</span> &lt;&lt; it-&gt;getIntensity() &lt;&lt; <span class="stringliteral">&quot;\n&quot;</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;</div>
<div class="line"><a name="l00227"></a><span class="lineno">  227</span>&#160;      <span class="comment">// Done.</span></div>
<div class="line"><a name="l00228"></a><span class="lineno">  228</span>&#160;      os.close();</div>
<div class="line"><a name="l00229"></a><span class="lineno">  229</span>&#160;    }</div>
<div class="line"><a name="l00230"></a><span class="lineno">  230</span>&#160;</div>
<div class="line"><a name="l00231"></a><span class="lineno">  231</span>&#160;  };</div>
<div class="line"><a name="l00232"></a><span class="lineno">  232</span>&#160;} <span class="comment">// namespace OpenMS</span></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;<span class="preprocessor">#endif // OPENMS_FORMAT_DTAFILE_H</span></div>
<div class="ttc" id="classOpenMS_1_1String_html"><div class="ttname"><a href="classOpenMS_1_1String.html">OpenMS::String</a></div><div class="ttdoc">A more convenient string class. </div><div class="ttdef"><b>Definition:</b> String.h:56</div></div>
<div class="ttc" id="classOpenMS_1_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>
<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_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>
<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>
<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>
<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_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>
<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>
<div class="ttc" id="File_8h_html"><div class="ttname"><a href="File_8h.html">File.h</a></div></div>
<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 &amp;filename, SpectrumType &amp;spectrum)</div><div class="ttdoc">Loads a DTA file to a spectrum. </div><div class="ttdef"><b>Definition:</b> DTAFile.h:76</div></div>
<div class="ttc" id="Constants_8h_html"><div class="ttname"><a href="Constants_8h.html">Constants.h</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_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="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 &amp;file)</div><div class="ttdoc">Returns the basename of the file (without the path). </div></div>
<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 &amp;filename, const SpectrumType &amp;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>
<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="Precursor_8h_html"><div class="ttname"><a href="Precursor_8h.html">Precursor.h</a></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_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>
<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>
<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_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>
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<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 11:19:13 using doxygen 1.8.5</font></TD>
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