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<a href="MS2File_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: Andreas Bertsch $</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_MS2FILE_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_MS2FILE_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="Exception_8h.html">OpenMS/CONCEPT/Exception.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="File_8h.html">OpenMS/SYSTEM/File.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="ProgressLogger_8h.html">OpenMS/CONCEPT/ProgressLogger.h</a>&gt;</span></div>
<div class="line"><a name="l00042"></a><span class="lineno">   42</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="DocumentIdentifier_8h.html">OpenMS/METADATA/DocumentIdentifier.h</a>&gt;</span></div>
<div class="line"><a name="l00043"></a><span class="lineno">   43</span>&#160;</div>
<div class="line"><a name="l00044"></a><span class="lineno">   44</span>&#160;<span class="preprocessor">#include &lt;vector&gt;</span></div>
<div class="line"><a name="l00045"></a><span class="lineno">   45</span>&#160;<span class="preprocessor">#include &lt;fstream&gt;</span></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">namespace </span>OpenMS</div>
<div class="line"><a name="l00048"></a><span class="lineno">   48</span>&#160;{</div>
<div class="line"><a name="l00065"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MS2File.html">   65</a></span>&#160;  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1MS2File.html">MS2File</a> :</div>
<div class="line"><a name="l00066"></a><span class="lineno">   66</span>&#160;    <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a></div>
<div class="line"><a name="l00067"></a><span class="lineno">   67</span>&#160;  {</div>
<div class="line"><a name="l00068"></a><span class="lineno">   68</span>&#160;<span class="keyword">public</span>:</div>
<div class="line"><a name="l00069"></a><span class="lineno">   69</span>&#160;</div>
<div class="line"><a name="l00071"></a><span class="lineno">   71</span>&#160;    <a class="code" href="classOpenMS_1_1MS2File.html">MS2File</a>();</div>
<div class="line"><a name="l00072"></a><span class="lineno">   72</span>&#160;</div>
<div class="line"><a name="l00074"></a><span class="lineno">   74</span>&#160;    <span class="keyword">virtual</span> ~<a class="code" href="classOpenMS_1_1MS2File.html">MS2File</a>();</div>
<div class="line"><a name="l00075"></a><span class="lineno">   75</span>&#160;</div>
<div class="line"><a name="l00076"></a><span class="lineno">   76</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">typename</span> MapType&gt;</div>
<div class="line"><a name="l00077"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MS2File.html#a98bebe67b8b06a9a67a3654d631355b4">   77</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1MS2File.html#a98bebe67b8b06a9a67a3654d631355b4">load</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; filename, MapType &amp; exp)</div>
<div class="line"><a name="l00078"></a><span class="lineno">   78</span>&#160;    {</div>
<div class="line"><a name="l00079"></a><span class="lineno">   79</span>&#160;      <span class="comment">//startProgress(0,0,&quot;loading DTA2D file&quot;);</span></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">if</span> (!<a class="code" href="classOpenMS_1_1File.html#a103bc592f26fed81f56f2f92b7ab5063">File::exists</a>(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;        <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="l00084"></a><span class="lineno">   84</span>&#160;      }</div>
<div class="line"><a name="l00085"></a><span class="lineno">   85</span>&#160;      <span class="keywordflow">if</span> (!<a class="code" href="classOpenMS_1_1File.html#abd34aea245381ce44044c36ce1895470">File::readable</a>(filename))</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="keywordflow">throw</span> <a class="code" href="classOpenMS_1_1Exception_1_1FileNotReadable.html">Exception::FileNotReadable</a>(__FILE__, __LINE__, __PRETTY_FUNCTION__, filename);</div>
<div class="line"><a name="l00088"></a><span class="lineno">   88</span>&#160;      }</div>
<div class="line"><a name="l00089"></a><span class="lineno">   89</span>&#160;</div>
<div class="line"><a name="l00090"></a><span class="lineno">   90</span>&#160;      exp.reset();</div>
<div class="line"><a name="l00091"></a><span class="lineno">   91</span>&#160;</div>
<div class="line"><a name="l00092"></a><span class="lineno">   92</span>&#160;      <span class="comment">//set DocumentIdentifier</span></div>
<div class="line"><a name="l00093"></a><span class="lineno">   93</span>&#160;      exp.setLoadedFileType(filename);</div>
<div class="line"><a name="l00094"></a><span class="lineno">   94</span>&#160;      exp.setLoadedFilePath(filename);</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;      std::ifstream in(filename.c_str());</div>
<div class="line"><a name="l00097"></a><span class="lineno">   97</span>&#160;</div>
<div class="line"><a name="l00098"></a><span class="lineno">   98</span>&#160;      <a class="code" href="classunsigned_01int.html">UInt</a> spectrum_number = 0;</div>
<div class="line"><a name="l00099"></a><span class="lineno">   99</span>&#160;      <span class="keyword">typename</span> MapType::SpectrumType spec;</div>
<div class="line"><a name="l00100"></a><span class="lineno">  100</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="l00101"></a><span class="lineno">  101</span>&#160;</div>
<div class="line"><a name="l00102"></a><span class="lineno">  102</span>&#160;      <a class="code" href="classOpenMS_1_1String.html">String</a> line;</div>
<div class="line"><a name="l00103"></a><span class="lineno">  103</span>&#160;      <span class="keywordtype">bool</span> first_spec(<span class="keyword">true</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="comment">// line number counter</span></div>
<div class="line"><a name="l00106"></a><span class="lineno">  106</span>&#160;      <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> line_number = 0;</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="keywordflow">while</span> (getline(in, line, <span class="charliteral">&#39;\n&#39;</span>))</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_number;</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;        line.<a class="code" href="classOpenMS_1_1String.html#a86864c88ee12eb322f1645f238c1dbe5">trim</a>();</div>
<div class="line"><a name="l00113"></a><span class="lineno">  113</span>&#160;        <span class="keywordflow">if</span> (line.empty()) <span class="keywordflow">continue</span>;</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;        <span class="comment">// header</span></div>
<div class="line"><a name="l00116"></a><span class="lineno">  116</span>&#160;        <span class="keywordflow">if</span> (line[0] == <span class="charliteral">&#39;H&#39;</span>)</div>
<div class="line"><a name="l00117"></a><span class="lineno">  117</span>&#160;        {</div>
<div class="line"><a name="l00118"></a><span class="lineno">  118</span>&#160;          <span class="keywordflow">continue</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;</div>
<div class="line"><a name="l00121"></a><span class="lineno">  121</span>&#160;        <span class="comment">// scan</span></div>
<div class="line"><a name="l00122"></a><span class="lineno">  122</span>&#160;        <span class="keywordflow">if</span> (line[0] == <span class="charliteral">&#39;S&#39;</span>)</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">if</span> (!first_spec)</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;            spec.setMSLevel(2);</div>
<div class="line"><a name="l00127"></a><span class="lineno">  127</span>&#160;            spec.setNativeID(<a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;index=&quot;</span>) + (spectrum_number++));</div>
<div class="line"><a name="l00128"></a><span class="lineno">  128</span>&#160;            exp.addSpectrum(spec);</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;          <span class="keywordflow">else</span></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;            first_spec = <span class="keyword">false</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;          spec.clear(<span class="keyword">true</span>);</div>
<div class="line"><a name="l00135"></a><span class="lineno">  135</span>&#160;          line.<a class="code" href="classOpenMS_1_1String.html#a23eb8a9a84f24127e87e0fb41076254c">simplify</a>();</div>
<div class="line"><a name="l00136"></a><span class="lineno">  136</span>&#160;          std::vector&lt;String&gt; split;</div>
<div class="line"><a name="l00137"></a><span class="lineno">  137</span>&#160;          line.<a class="code" href="classOpenMS_1_1String.html#ae580d960e12c7f0ebc5c95931cf39ad5">split</a>(<span class="charliteral">&#39; &#39;</span>, split);</div>
<div class="line"><a name="l00138"></a><span class="lineno">  138</span>&#160;          <span class="keywordflow">if</span> (split.size() != 4)</div>
<div class="line"><a name="l00139"></a><span class="lineno">  139</span>&#160;          {</div>
<div class="line"><a name="l00140"></a><span class="lineno">  140</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;line (&quot;</span> + <a class="code" href="classOpenMS_1_1String.html">String</a>(line_number) + <span class="stringliteral">&quot;) &#39;&quot;</span> + line  + <span class="stringliteral">&quot;&#39; should contain four values, got &quot;</span> + <a class="code" href="classOpenMS_1_1String.html">String</a>(split.size()) + <span class="stringliteral">&quot;!&quot;</span>, <span class="stringliteral">&quot;&quot;</span>);</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;          spec.getPrecursors().resize(1);</div>
<div class="line"><a name="l00143"></a><span class="lineno">  143</span>&#160;          spec.getPrecursors()[0].setMZ(split[3].toDouble());</div>
<div class="line"><a name="l00144"></a><span class="lineno">  144</span>&#160;          <span class="keywordflow">continue</span>;</div>
<div class="line"><a name="l00145"></a><span class="lineno">  145</span>&#160;        }</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;        <span class="comment">// charge-independent analysis</span></div>
<div class="line"><a name="l00148"></a><span class="lineno">  148</span>&#160;        <span class="keywordflow">if</span> (line[0] == <span class="charliteral">&#39;I&#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">continue</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;</div>
<div class="line"><a name="l00153"></a><span class="lineno">  153</span>&#160;        <span class="comment">// charge specification</span></div>
<div class="line"><a name="l00154"></a><span class="lineno">  154</span>&#160;        <span class="keywordflow">if</span> (line[0] == <span class="charliteral">&#39;Z&#39;</span>)</div>
<div class="line"><a name="l00155"></a><span class="lineno">  155</span>&#160;        {</div>
<div class="line"><a name="l00156"></a><span class="lineno">  156</span>&#160;          <span class="keywordflow">continue</span>;</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;</div>
<div class="line"><a name="l00159"></a><span class="lineno">  159</span>&#160;        <span class="comment">// charge-dependent analysis</span></div>
<div class="line"><a name="l00160"></a><span class="lineno">  160</span>&#160;        <span class="keywordflow">if</span> (line[0] == <span class="charliteral">&#39;D&#39;</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="keywordflow">continue</span>;</div>
<div class="line"><a name="l00163"></a><span class="lineno">  163</span>&#160;        }</div>
<div class="line"><a name="l00164"></a><span class="lineno">  164</span>&#160;</div>
<div class="line"><a name="l00165"></a><span class="lineno">  165</span>&#160;        <span class="comment">// yet another peak, hopefully</span></div>
<div class="line"><a name="l00166"></a><span class="lineno">  166</span>&#160;        line.<a class="code" href="classOpenMS_1_1String.html#a23eb8a9a84f24127e87e0fb41076254c">simplify</a>();</div>
<div class="line"><a name="l00167"></a><span class="lineno">  167</span>&#160;        std::vector&lt;String&gt; split;</div>
<div class="line"><a name="l00168"></a><span class="lineno">  168</span>&#160;        line.<a class="code" href="classOpenMS_1_1String.html#ae580d960e12c7f0ebc5c95931cf39ad5">split</a>(<span class="charliteral">&#39; &#39;</span>, split);</div>
<div class="line"><a name="l00169"></a><span class="lineno">  169</span>&#160;        <span class="keywordflow">if</span> (split.size() != 2)</div>
<div class="line"><a name="l00170"></a><span class="lineno">  170</span>&#160;        {</div>
<div class="line"><a name="l00171"></a><span class="lineno">  171</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;line (&quot;</span> + <a class="code" href="classOpenMS_1_1String.html">String</a>(line_number) + <span class="stringliteral">&quot;) &#39;&quot;</span> + line  + <span class="stringliteral">&quot;&#39; should contain two values, got &quot;</span> + <a class="code" href="classOpenMS_1_1String.html">String</a>(split.size()) + <span class="stringliteral">&quot;!&quot;</span>, <span class="stringliteral">&quot;&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;</div>
<div class="line"><a name="l00174"></a><span class="lineno">  174</span>&#160;        <span class="keywordflow">try</span></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;          p.setPosition(split[0].toDouble());</div>
<div class="line"><a name="l00177"></a><span class="lineno">  177</span>&#160;          p.setIntensity(split[1].toFloat());</div>
<div class="line"><a name="l00178"></a><span class="lineno">  178</span>&#160;        }</div>
<div class="line"><a name="l00179"></a><span class="lineno">  179</span>&#160;        <span class="keywordflow">catch</span> (<a class="code" href="classOpenMS_1_1Exception_1_1ConversionError.html">Exception::ConversionError</a> <span class="comment">/*&amp;e*/</span>)</div>
<div class="line"><a name="l00180"></a><span class="lineno">  180</span>&#160;        {</div>
<div class="line"><a name="l00181"></a><span class="lineno">  181</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;ConversionError: line (&quot;</span> + <a class="code" href="classOpenMS_1_1String.html">String</a>(line_number) + <span class="stringliteral">&quot;) &#39;&quot;</span> + line  + <span class="stringliteral">&quot;&#39; does not contain two numbers!&quot;</span>, <span class="stringliteral">&quot;&quot;</span>);</div>
<div class="line"><a name="l00182"></a><span class="lineno">  182</span>&#160;        }</div>
<div class="line"><a name="l00183"></a><span class="lineno">  183</span>&#160;        spec.push_back(p);</div>
<div class="line"><a name="l00184"></a><span class="lineno">  184</span>&#160;      }</div>
<div class="line"><a name="l00185"></a><span class="lineno">  185</span>&#160;</div>
<div class="line"><a name="l00186"></a><span class="lineno">  186</span>&#160;      <span class="keywordflow">if</span> (!first_spec)</div>
<div class="line"><a name="l00187"></a><span class="lineno">  187</span>&#160;      {</div>
<div class="line"><a name="l00188"></a><span class="lineno">  188</span>&#160;        spec.setMSLevel(2);</div>
<div class="line"><a name="l00189"></a><span class="lineno">  189</span>&#160;        spec.setNativeID(<a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;index=&quot;</span>) + (spectrum_number++));</div>
<div class="line"><a name="l00190"></a><span class="lineno">  190</span>&#160;        exp.addSpectrum(spec);</div>
<div class="line"><a name="l00191"></a><span class="lineno">  191</span>&#160;      }</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;</div>
<div class="line"><a name="l00194"></a><span class="lineno">  194</span>&#160;    <span class="comment">/*</span></div>
<div class="line"><a name="l00195"></a><span class="lineno">  195</span>&#160;<span class="comment">    template &lt;typename MapType&gt; void store(const String&amp; filename, MapType&amp; map)</span></div>
<div class="line"><a name="l00196"></a><span class="lineno">  196</span>&#160;<span class="comment">    {</span></div>
<div class="line"><a name="l00197"></a><span class="lineno">  197</span>&#160;<span class="comment"></span></div>
<div class="line"><a name="l00198"></a><span class="lineno">  198</span>&#160;<span class="comment">    }</span></div>
<div class="line"><a name="l00199"></a><span class="lineno">  199</span>&#160;<span class="comment">    */</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;<span class="keyword">protected</span>:</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;  };</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">// namespace OpenMS</span></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="preprocessor">#endif // OPENMS_FORMAT_MS2FILE_H</span></div>
<div class="ttc" id="classOpenMS_1_1String_html_a23eb8a9a84f24127e87e0fb41076254c"><div class="ttname"><a href="classOpenMS_1_1String.html#a23eb8a9a84f24127e87e0fb41076254c">OpenMS::String::simplify</a></div><div class="ttdeci">String &amp; simplify()</div><div class="ttdoc">merges subsequent whitespaces to one blank character </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="DocumentIdentifier_8h_html"><div class="ttname"><a href="DocumentIdentifier_8h.html">DocumentIdentifier.h</a></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_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="File_8h_html"><div class="ttname"><a href="File_8h.html">File.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1Exception_1_1FileNotReadable_html"><div class="ttname"><a href="classOpenMS_1_1Exception_1_1FileNotReadable.html">OpenMS::Exception::FileNotReadable</a></div><div class="ttdoc">File not readable exception. </div><div class="ttdef"><b>Definition:</b> Exception.h:538</div></div>
<div class="ttc" id="classOpenMS_1_1File_html_a103bc592f26fed81f56f2f92b7ab5063"><div class="ttname"><a href="classOpenMS_1_1File.html#a103bc592f26fed81f56f2f92b7ab5063">OpenMS::File::exists</a></div><div class="ttdeci">static bool exists(const String &amp;file)</div><div class="ttdoc">Method used to test if a file exists. </div></div>
<div class="ttc" id="classOpenMS_1_1MS2File_html_a98bebe67b8b06a9a67a3654d631355b4"><div class="ttname"><a href="classOpenMS_1_1MS2File.html#a98bebe67b8b06a9a67a3654d631355b4">OpenMS::MS2File::load</a></div><div class="ttdeci">void load(const String &amp;filename, MapType &amp;exp)</div><div class="ttdef"><b>Definition:</b> MS2File.h:77</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_1ConversionError_html"><div class="ttname"><a href="classOpenMS_1_1Exception_1_1ConversionError.html">OpenMS::Exception::ConversionError</a></div><div class="ttdoc">Invalid conversion exception. </div><div class="ttdef"><b>Definition:</b> Exception.h:363</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_1MS2File_html"><div class="ttname"><a href="classOpenMS_1_1MS2File.html">OpenMS::MS2File</a></div><div class="ttdoc">MS2 input file adapter. </div><div class="ttdef"><b>Definition:</b> MS2File.h:65</div></div>
<div class="ttc" id="Exception_8h_html"><div class="ttname"><a href="Exception_8h.html">Exception.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1File_html_abd34aea245381ce44044c36ce1895470"><div class="ttname"><a href="classOpenMS_1_1File.html#abd34aea245381ce44044c36ce1895470">OpenMS::File::readable</a></div><div class="ttdeci">static bool readable(const String &amp;file)</div><div class="ttdoc">Return true if the file exists and is readable. </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 11:19:17 using doxygen 1.8.5</font></TD>
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