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<a href="FileHandler_8h.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="comment">// OpenMS -- Open-Source Mass Spectrometry</span></div>
<div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="comment">// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,</span></div>
<div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="comment">// ETH Zurich, and Freie Universitaet Berlin 2002-2013.</span></div>
<div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="comment">//</span></div>
<div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="comment">// This software is released under a three-clause BSD license:</span></div>
<div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="comment">// * Redistributions of source code must retain the above copyright</span></div>
<div class="line"><a name="l00009"></a><span class="lineno"> 9</span> <span class="comment">// notice, this list of conditions and the following disclaimer.</span></div>
<div class="line"><a name="l00010"></a><span class="lineno"> 10</span> <span class="comment">// * Redistributions in binary form must reproduce the above copyright</span></div>
<div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="comment">// notice, this list of conditions and the following disclaimer in the</span></div>
<div class="line"><a name="l00012"></a><span class="lineno"> 12</span> <span class="comment">// documentation and/or other materials provided with the distribution.</span></div>
<div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="comment">// * Neither the name of any author or any participating institution</span></div>
<div class="line"><a name="l00014"></a><span class="lineno"> 14</span> <span class="comment">// may be used to endorse or promote products derived from this software</span></div>
<div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="comment">// without specific prior written permission.</span></div>
<div class="line"><a name="l00016"></a><span class="lineno"> 16</span> <span class="comment">// For a full list of authors, refer to the file AUTHORS.</span></div>
<div class="line"><a name="l00017"></a><span class="lineno"> 17</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00018"></a><span class="lineno"> 18</span> <span class="comment">// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"</span></div>
<div class="line"><a name="l00019"></a><span class="lineno"> 19</span> <span class="comment">// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE</span></div>
<div class="line"><a name="l00020"></a><span class="lineno"> 20</span> <span class="comment">// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE</span></div>
<div class="line"><a name="l00021"></a><span class="lineno"> 21</span> <span class="comment">// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING</span></div>
<div class="line"><a name="l00022"></a><span class="lineno"> 22</span> <span class="comment">// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,</span></div>
<div class="line"><a name="l00023"></a><span class="lineno"> 23</span> <span class="comment">// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,</span></div>
<div class="line"><a name="l00024"></a><span class="lineno"> 24</span> <span class="comment">// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;</span></div>
<div class="line"><a name="l00025"></a><span class="lineno"> 25</span> <span class="comment">// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,</span></div>
<div class="line"><a name="l00026"></a><span class="lineno"> 26</span> <span class="comment">// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR</span></div>
<div class="line"><a name="l00027"></a><span class="lineno"> 27</span> <span class="comment">// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF</span></div>
<div class="line"><a name="l00028"></a><span class="lineno"> 28</span> <span class="comment">// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</span></div>
<div class="line"><a name="l00029"></a><span class="lineno"> 29</span> <span class="comment">//</span></div>
<div class="line"><a name="l00030"></a><span class="lineno"> 30</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00031"></a><span class="lineno"> 31</span> <span class="comment">// $Maintainer: Stephan Aiche $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno"> 32</span> <span class="comment">// $Authors: Marc Sturm $</span></div>
<div class="line"><a name="l00033"></a><span class="lineno"> 33</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00034"></a><span class="lineno"> 34</span> </div>
<div class="line"><a name="l00035"></a><span class="lineno"> 35</span> <span class="preprocessor">#ifndef OPENMS_FORMAT_FILEHANDLER_H</span></div>
<div class="line"><a name="l00036"></a><span class="lineno"> 36</span> <span class="preprocessor"></span><span class="preprocessor">#define OPENMS_FORMAT_FILEHANDLER_H</span></div>
<div class="line"><a name="l00037"></a><span class="lineno"> 37</span> <span class="preprocessor"></span></div>
<div class="line"><a name="l00038"></a><span class="lineno"> 38</span> <span class="preprocessor">#include <OpenMS/config.h></span></div>
<div class="line"><a name="l00039"></a><span class="lineno"> 39</span> <span class="preprocessor">#include <<a class="code" href="FileTypes_8h.html">OpenMS/FORMAT/FileTypes.h</a>></span></div>
<div class="line"><a name="l00040"></a><span class="lineno"> 40</span> </div>
<div class="line"><a name="l00041"></a><span class="lineno"> 41</span> <span class="preprocessor">#include <<a class="code" href="DTAFile_8h.html">OpenMS/FORMAT/DTAFile.h</a>></span></div>
<div class="line"><a name="l00042"></a><span class="lineno"> 42</span> <span class="preprocessor">#include <<a class="code" href="DTA2DFile_8h.html">OpenMS/FORMAT/DTA2DFile.h</a>></span></div>
<div class="line"><a name="l00043"></a><span class="lineno"> 43</span> <span class="preprocessor">#include <<a class="code" href="MzXMLFile_8h.html">OpenMS/FORMAT/MzXMLFile.h</a>></span></div>
<div class="line"><a name="l00044"></a><span class="lineno"> 44</span> <span class="preprocessor">#include <<a class="code" href="MzMLFile_8h.html">OpenMS/FORMAT/MzMLFile.h</a>></span></div>
<div class="line"><a name="l00045"></a><span class="lineno"> 45</span> <span class="preprocessor">#include <<a class="code" href="FeatureXMLFile_8h.html">OpenMS/FORMAT/FeatureXMLFile.h</a>></span></div>
<div class="line"><a name="l00046"></a><span class="lineno"> 46</span> <span class="preprocessor">#include <<a class="code" href="MzDataFile_8h.html">OpenMS/FORMAT/MzDataFile.h</a>></span></div>
<div class="line"><a name="l00047"></a><span class="lineno"> 47</span> <span class="preprocessor">#include <<a class="code" href="MascotGenericFile_8h.html">OpenMS/FORMAT/MascotGenericFile.h</a>></span></div>
<div class="line"><a name="l00048"></a><span class="lineno"> 48</span> <span class="preprocessor">#include <<a class="code" href="MS2File_8h.html">OpenMS/FORMAT/MS2File.h</a>></span></div>
<div class="line"><a name="l00049"></a><span class="lineno"> 49</span> <span class="preprocessor">#include <<a class="code" href="XMassFile_8h.html">OpenMS/FORMAT/XMassFile.h</a>></span></div>
<div class="line"><a name="l00050"></a><span class="lineno"> 50</span> </div>
<div class="line"><a name="l00051"></a><span class="lineno"> 51</span> <span class="preprocessor">#include <<a class="code" href="MsInspectFile_8h.html">OpenMS/FORMAT/MsInspectFile.h</a>></span></div>
<div class="line"><a name="l00052"></a><span class="lineno"> 52</span> <span class="preprocessor">#include <<a class="code" href="SpecArrayFile_8h.html">OpenMS/FORMAT/SpecArrayFile.h</a>></span></div>
<div class="line"><a name="l00053"></a><span class="lineno"> 53</span> <span class="preprocessor">#include <<a class="code" href="KroenikFile_8h.html">OpenMS/FORMAT/KroenikFile.h</a>></span></div>
<div class="line"><a name="l00054"></a><span class="lineno"> 54</span> </div>
<div class="line"><a name="l00055"></a><span class="lineno"> 55</span> <span class="preprocessor">#include <<a class="code" href="ChromatogramTools_8h.html">OpenMS/KERNEL/ChromatogramTools.h</a>></span></div>
<div class="line"><a name="l00056"></a><span class="lineno"> 56</span> <span class="preprocessor">#include <<a class="code" href="ProgressLogger_8h.html">OpenMS/CONCEPT/ProgressLogger.h</a>></span></div>
<div class="line"><a name="l00057"></a><span class="lineno"> 57</span> </div>
<div class="line"><a name="l00058"></a><span class="lineno"> 58</span> <span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00059"></a><span class="lineno"> 59</span> {</div>
<div class="line"><a name="l00073"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FileHandler.html"> 73</a></span>  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1FileHandler.html">FileHandler</a></div>
<div class="line"><a name="l00074"></a><span class="lineno"> 74</span>  {</div>
<div class="line"><a name="l00075"></a><span class="lineno"> 75</span> <span class="keyword">public</span>:</div>
<div class="line"><a name="l00084"></a><span class="lineno"> 84</span>  <span class="keyword">static</span> <a class="code" href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7">FileTypes::Type</a> getType(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& filename);</div>
<div class="line"><a name="l00085"></a><span class="lineno"> 85</span> </div>
<div class="line"><a name="l00086"></a><span class="lineno"> 86</span> </div>
<div class="line"><a name="l00088"></a><span class="lineno"> 88</span>  <span class="keyword">static</span> <a class="code" href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7">FileTypes::Type</a> getTypeByFileName(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& filename);</div>
<div class="line"><a name="l00089"></a><span class="lineno"> 89</span> </div>
<div class="line"><a name="l00095"></a><span class="lineno"> 95</span>  <span class="keyword">static</span> <a class="code" href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7">FileTypes::Type</a> getTypeByContent(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& filename);</div>
<div class="line"><a name="l00096"></a><span class="lineno"> 96</span> </div>
<div class="line"><a name="l00098"></a><span class="lineno"> 98</span>  <span class="keyword">static</span> <span class="keywordtype">bool</span> isSupported(<a class="code" href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7">FileTypes::Type</a> type);</div>
<div class="line"><a name="l00099"></a><span class="lineno"> 99</span> </div>
<div class="line"><a name="l00101"></a><span class="lineno"> 101</span>  <a class="code" href="classOpenMS_1_1PeakFileOptions.html">PeakFileOptions</a>& getOptions();</div>
<div class="line"><a name="l00102"></a><span class="lineno"> 102</span> </div>
<div class="line"><a name="l00104"></a><span class="lineno"> 104</span>  <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1PeakFileOptions.html">PeakFileOptions</a>& getOptions() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00105"></a><span class="lineno"> 105</span> </div>
<div class="line"><a name="l00120"></a><span class="lineno"> 120</span>  <span class="keyword">template</span> <<span class="keyword">class</span> PeakType></div>
<div class="line"><a name="l00121"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FileHandler.html#a408091416e0e1f6019abd59bdb6a9269"> 121</a></span>  <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1FileHandler.html#a408091416e0e1f6019abd59bdb6a9269">loadExperiment</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& filename, <a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment<PeakType></a>& exp, <a class="code" href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7">FileTypes::Type</a> force_type = <a class="code" href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7a6ce26a62afab55d7606ad4e92428b30c">FileTypes::UNKNOWN</a>, <a class="code" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87c">ProgressLogger::LogType</a> log = <a class="code" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87cac157bdf0b85a40d2619cbc8bc1ae5fe2">ProgressLogger::NONE</a>, <span class="keyword">const</span> <span class="keywordtype">bool</span> compute_hash = <span class="keyword">true</span>)</div>
<div class="line"><a name="l00122"></a><span class="lineno"> 122</span>  {</div>
<div class="line"><a name="l00123"></a><span class="lineno"> 123</span>  <span class="comment">//determine file type</span></div>
<div class="line"><a name="l00124"></a><span class="lineno"> 124</span>  <a class="code" href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7">FileTypes::Type</a> type;</div>
<div class="line"><a name="l00125"></a><span class="lineno"> 125</span>  <span class="keywordflow">if</span> (force_type != <a class="code" href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7a6ce26a62afab55d7606ad4e92428b30c">FileTypes::UNKNOWN</a>)</div>
<div class="line"><a name="l00126"></a><span class="lineno"> 126</span>  {</div>
<div class="line"><a name="l00127"></a><span class="lineno"> 127</span>  type = force_type;</div>
<div class="line"><a name="l00128"></a><span class="lineno"> 128</span>  }</div>
<div class="line"><a name="l00129"></a><span class="lineno"> 129</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00130"></a><span class="lineno"> 130</span>  {</div>
<div class="line"><a name="l00131"></a><span class="lineno"> 131</span>  <span class="keywordflow">try</span></div>
<div class="line"><a name="l00132"></a><span class="lineno"> 132</span>  {</div>
<div class="line"><a name="l00133"></a><span class="lineno"> 133</span>  type = getType(filename);</div>
<div class="line"><a name="l00134"></a><span class="lineno"> 134</span>  }</div>
<div class="line"><a name="l00135"></a><span class="lineno"> 135</span>  <span class="keywordflow">catch</span> (<a class="code" href="classOpenMS_1_1Exception_1_1FileNotFound.html">Exception::FileNotFound</a>)</div>
<div class="line"><a name="l00136"></a><span class="lineno"> 136</span>  {</div>
<div class="line"><a name="l00137"></a><span class="lineno"> 137</span>  <span class="keywordflow">return</span> <span class="keyword">false</span>;</div>
<div class="line"><a name="l00138"></a><span class="lineno"> 138</span>  }</div>
<div class="line"><a name="l00139"></a><span class="lineno"> 139</span>  }</div>
<div class="line"><a name="l00140"></a><span class="lineno"> 140</span> </div>
<div class="line"><a name="l00141"></a><span class="lineno"> 141</span>  <span class="comment">//load right file</span></div>
<div class="line"><a name="l00142"></a><span class="lineno"> 142</span>  <span class="keywordflow">switch</span> (type)</div>
<div class="line"><a name="l00143"></a><span class="lineno"> 143</span>  {</div>
<div class="line"><a name="l00144"></a><span class="lineno"> 144</span>  <span class="keywordflow">case</span> <a class="code" href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7ad8654d9b2a9c38ece897bfbdd8152214">FileTypes::DTA</a>:</div>
<div class="line"><a name="l00145"></a><span class="lineno"> 145</span>  exp.<a class="code" href="classOpenMS_1_1MSExperiment.html#ad20897c5c8bd47f5d4005989bead0e55">reset</a>();</div>
<div class="line"><a name="l00146"></a><span class="lineno"> 146</span>  exp.<a class="code" href="classOpenMS_1_1MSExperiment.html#ac2bc824d6ff2633ec34793c9e918d479">resize</a>(1);</div>
<div class="line"><a name="l00147"></a><span class="lineno"> 147</span>  <a class="code" href="classOpenMS_1_1DTAFile.html">DTAFile</a>().<a class="code" href="classOpenMS_1_1DTAFile.html#a583280bb0e47a5d57b337d6440c96b73">load</a>(filename, exp[0]);</div>
<div class="line"><a name="l00148"></a><span class="lineno"> 148</span>  <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l00149"></a><span class="lineno"> 149</span> </div>
<div class="line"><a name="l00150"></a><span class="lineno"> 150</span>  <span class="keywordflow">case</span> <a class="code" href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7a66c2f5cd90913752f565186657e85d84">FileTypes::DTA2D</a>:</div>
<div class="line"><a name="l00151"></a><span class="lineno"> 151</span>  {</div>
<div class="line"><a name="l00152"></a><span class="lineno"> 152</span>  <a class="code" href="classOpenMS_1_1DTA2DFile.html">DTA2DFile</a> f;</div>
<div class="line"><a name="l00153"></a><span class="lineno"> 153</span>  f.<a class="code" href="classOpenMS_1_1DTA2DFile.html#a819235ed2844f03df53f4983a7008f28">getOptions</a>() = options_;</div>
<div class="line"><a name="l00154"></a><span class="lineno"> 154</span>  f.<a class="code" href="classOpenMS_1_1ProgressLogger.html#acc3538c5284777d8702ccaefeb61e74c">setLogType</a>(log);</div>
<div class="line"><a name="l00155"></a><span class="lineno"> 155</span>  f.<a class="code" href="classOpenMS_1_1DTA2DFile.html#aed378b9a389ec00fa2b559bf7d3b710b">load</a>(filename, exp);</div>
<div class="line"><a name="l00156"></a><span class="lineno"> 156</span>  }</div>
<div class="line"><a name="l00157"></a><span class="lineno"> 157</span> </div>
<div class="line"><a name="l00158"></a><span class="lineno"> 158</span>  <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l00159"></a><span class="lineno"> 159</span> </div>
<div class="line"><a name="l00160"></a><span class="lineno"> 160</span>  <span class="keywordflow">case</span> <a class="code" href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7af8a53519bd415aacd429c4239bbfd66e">FileTypes::MZXML</a>:</div>
<div class="line"><a name="l00161"></a><span class="lineno"> 161</span>  {</div>
<div class="line"><a name="l00162"></a><span class="lineno"> 162</span>  <a class="code" href="classOpenMS_1_1MzXMLFile.html">MzXMLFile</a> f;</div>
<div class="line"><a name="l00163"></a><span class="lineno"> 163</span>  f.<a class="code" href="classOpenMS_1_1MzXMLFile.html#a819235ed2844f03df53f4983a7008f28">getOptions</a>() = options_;</div>
<div class="line"><a name="l00164"></a><span class="lineno"> 164</span>  f.<a class="code" href="classOpenMS_1_1ProgressLogger.html#acc3538c5284777d8702ccaefeb61e74c">setLogType</a>(log);</div>
<div class="line"><a name="l00165"></a><span class="lineno"> 165</span>  f.<a class="code" href="classOpenMS_1_1MzXMLFile.html#aed378b9a389ec00fa2b559bf7d3b710b">load</a>(filename, exp);</div>
<div class="line"><a name="l00166"></a><span class="lineno"> 166</span>  }</div>
<div class="line"><a name="l00167"></a><span class="lineno"> 167</span> </div>
<div class="line"><a name="l00168"></a><span class="lineno"> 168</span>  <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l00169"></a><span class="lineno"> 169</span> </div>
<div class="line"><a name="l00170"></a><span class="lineno"> 170</span>  <span class="keywordflow">case</span> <a class="code" href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7ae5b2d8f7eb59b2fc050e6bc3c1cba802">FileTypes::MZDATA</a>:</div>
<div class="line"><a name="l00171"></a><span class="lineno"> 171</span>  {</div>
<div class="line"><a name="l00172"></a><span class="lineno"> 172</span>  <a class="code" href="classOpenMS_1_1MzDataFile.html">MzDataFile</a> f;</div>
<div class="line"><a name="l00173"></a><span class="lineno"> 173</span>  f.<a class="code" href="classOpenMS_1_1MzDataFile.html#a819235ed2844f03df53f4983a7008f28">getOptions</a>() = options_;</div>
<div class="line"><a name="l00174"></a><span class="lineno"> 174</span>  f.<a class="code" href="classOpenMS_1_1ProgressLogger.html#acc3538c5284777d8702ccaefeb61e74c">setLogType</a>(log);</div>
<div class="line"><a name="l00175"></a><span class="lineno"> 175</span>  f.<a class="code" href="classOpenMS_1_1MzDataFile.html#aed378b9a389ec00fa2b559bf7d3b710b">load</a>(filename, exp);</div>
<div class="line"><a name="l00176"></a><span class="lineno"> 176</span>  }</div>
<div class="line"><a name="l00177"></a><span class="lineno"> 177</span>  <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l00178"></a><span class="lineno"> 178</span> </div>
<div class="line"><a name="l00179"></a><span class="lineno"> 179</span>  <span class="keywordflow">case</span> <a class="code" href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7ab5518cc16bd1f60ebbb47e681a56b75f">FileTypes::MZML</a>:</div>
<div class="line"><a name="l00180"></a><span class="lineno"> 180</span>  {</div>
<div class="line"><a name="l00181"></a><span class="lineno"> 181</span>  <a class="code" href="classOpenMS_1_1MzMLFile.html">MzMLFile</a> f;</div>
<div class="line"><a name="l00182"></a><span class="lineno"> 182</span>  f.<a class="code" href="classOpenMS_1_1MzMLFile.html#a819235ed2844f03df53f4983a7008f28">getOptions</a>() = options_;</div>
<div class="line"><a name="l00183"></a><span class="lineno"> 183</span>  f.<a class="code" href="classOpenMS_1_1ProgressLogger.html#acc3538c5284777d8702ccaefeb61e74c">setLogType</a>(log);</div>
<div class="line"><a name="l00184"></a><span class="lineno"> 184</span>  f.<a class="code" href="classOpenMS_1_1MzMLFile.html#aed378b9a389ec00fa2b559bf7d3b710b">load</a>(filename, exp);</div>
<div class="line"><a name="l00185"></a><span class="lineno"> 185</span>  <a class="code" href="classOpenMS_1_1ChromatogramTools.html">ChromatogramTools</a>().<a class="code" href="classOpenMS_1_1ChromatogramTools.html#af3ff28dcfb8f80c33a57605672ebb0b1">convertSpectraToChromatograms</a><<a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment<PeakType></a> >(exp, <span class="keyword">true</span>);</div>
<div class="line"><a name="l00186"></a><span class="lineno"> 186</span>  }</div>
<div class="line"><a name="l00187"></a><span class="lineno"> 187</span>  <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l00188"></a><span class="lineno"> 188</span> </div>
<div class="line"><a name="l00189"></a><span class="lineno"> 189</span>  <span class="keywordflow">case</span> <a class="code" href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7a29bb13323f25136faf82e418da451b26">FileTypes::MGF</a>:</div>
<div class="line"><a name="l00190"></a><span class="lineno"> 190</span>  {</div>
<div class="line"><a name="l00191"></a><span class="lineno"> 191</span>  <a class="code" href="classOpenMS_1_1MascotGenericFile.html">MascotGenericFile</a> f;</div>
<div class="line"><a name="l00192"></a><span class="lineno"> 192</span>  f.<a class="code" href="classOpenMS_1_1ProgressLogger.html#acc3538c5284777d8702ccaefeb61e74c">setLogType</a>(log);</div>
<div class="line"><a name="l00193"></a><span class="lineno"> 193</span>  f.<a class="code" href="classOpenMS_1_1MascotGenericFile.html#a98bebe67b8b06a9a67a3654d631355b4">load</a>(filename, exp);</div>
<div class="line"><a name="l00194"></a><span class="lineno"> 194</span>  }</div>
<div class="line"><a name="l00195"></a><span class="lineno"> 195</span> </div>
<div class="line"><a name="l00196"></a><span class="lineno"> 196</span>  <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l00197"></a><span class="lineno"> 197</span> </div>
<div class="line"><a name="l00198"></a><span class="lineno"> 198</span>  <span class="keywordflow">case</span> <a class="code" href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7ac59ebe001fb1923baf25b050436a5f15">FileTypes::MS2</a>:</div>
<div class="line"><a name="l00199"></a><span class="lineno"> 199</span>  {</div>
<div class="line"><a name="l00200"></a><span class="lineno"> 200</span>  <a class="code" href="classOpenMS_1_1MS2File.html">MS2File</a> f;</div>
<div class="line"><a name="l00201"></a><span class="lineno"> 201</span>  f.<a class="code" href="classOpenMS_1_1ProgressLogger.html#acc3538c5284777d8702ccaefeb61e74c">setLogType</a>(log);</div>
<div class="line"><a name="l00202"></a><span class="lineno"> 202</span>  f.<a class="code" href="classOpenMS_1_1MS2File.html#a98bebe67b8b06a9a67a3654d631355b4">load</a>(filename, exp);</div>
<div class="line"><a name="l00203"></a><span class="lineno"> 203</span>  }</div>
<div class="line"><a name="l00204"></a><span class="lineno"> 204</span> </div>
<div class="line"><a name="l00205"></a><span class="lineno"> 205</span>  <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l00206"></a><span class="lineno"> 206</span> </div>
<div class="line"><a name="l00207"></a><span class="lineno"> 207</span>  <span class="keywordflow">case</span> <a class="code" href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7a87b48e9729223183349bdfb171076285">FileTypes::XMASS</a>:</div>
<div class="line"><a name="l00208"></a><span class="lineno"> 208</span>  exp.<a class="code" href="classOpenMS_1_1MSExperiment.html#ad20897c5c8bd47f5d4005989bead0e55">reset</a>();</div>
<div class="line"><a name="l00209"></a><span class="lineno"> 209</span>  exp.<a class="code" href="classOpenMS_1_1MSExperiment.html#ac2bc824d6ff2633ec34793c9e918d479">resize</a>(1);</div>
<div class="line"><a name="l00210"></a><span class="lineno"> 210</span>  <a class="code" href="classOpenMS_1_1XMassFile.html">XMassFile</a>().<a class="code" href="classOpenMS_1_1XMassFile.html#a865164e026ef00fa12377c1d63613613">load</a>(filename, exp[0]);</div>
<div class="line"><a name="l00211"></a><span class="lineno"> 211</span>  <a class="code" href="classOpenMS_1_1XMassFile.html">XMassFile</a>().<a class="code" href="classOpenMS_1_1XMassFile.html#a43556a513eaa5395c068a7c9874cc6d1">importExperimentalSettings</a>(filename, exp);</div>
<div class="line"><a name="l00212"></a><span class="lineno"> 212</span> </div>
<div class="line"><a name="l00213"></a><span class="lineno"> 213</span>  <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l00214"></a><span class="lineno"> 214</span> </div>
<div class="line"><a name="l00215"></a><span class="lineno"> 215</span>  <span class="keywordflow">default</span>:</div>
<div class="line"><a name="l00216"></a><span class="lineno"> 216</span>  <span class="keywordflow">return</span> <span class="keyword">false</span>;</div>
<div class="line"><a name="l00217"></a><span class="lineno"> 217</span> </div>
<div class="line"><a name="l00218"></a><span class="lineno"> 218</span>  <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l00219"></a><span class="lineno"> 219</span>  }</div>
<div class="line"><a name="l00220"></a><span class="lineno"> 220</span> </div>
<div class="line"><a name="l00221"></a><span class="lineno"> 221</span>  <a class="code" href="classOpenMS_1_1SourceFile.html">SourceFile</a> src_file;</div>
<div class="line"><a name="l00222"></a><span class="lineno"> 222</span>  src_file.<a class="code" href="classOpenMS_1_1SourceFile.html#af0a7eddbacf20c4f4045b671df6b0fe7">setNameOfFile</a>(<a class="code" href="classOpenMS_1_1File.html#a6487771c96fec9db032960c91864884e">File::basename</a>(filename));</div>
<div class="line"><a name="l00223"></a><span class="lineno"> 223</span>  src_file.<a class="code" href="classOpenMS_1_1SourceFile.html#a2edd9a092842480801a9738a3a514fb3">setPathToFile</a>(<a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">"file:///"</span>) + <a class="code" href="classOpenMS_1_1File.html#a43bdcb2e5cb18da64e25b2467c8fdcaa">File::path</a>(filename));</div>
<div class="line"><a name="l00224"></a><span class="lineno"> 224</span>  <span class="comment">// this is more complicated since the data formats allowed by mzML are very verbose.</span></div>
<div class="line"><a name="l00225"></a><span class="lineno"> 225</span>  <span class="comment">// this is prone to changing CV's... our writer will fall back to a default if the name given here is invalid.</span></div>
<div class="line"><a name="l00226"></a><span class="lineno"> 226</span>  src_file.<a class="code" href="classOpenMS_1_1SourceFile.html#a2d47bfad02d5ce05dcfab38bc1b21400">setFileType</a>(<a class="code" href="structOpenMS_1_1FileTypes.html#a854df315fb804a3fba0232334a7f1d0f">FileTypes::typeToMZML</a>(type));</div>
<div class="line"><a name="l00227"></a><span class="lineno"> 227</span> </div>
<div class="line"><a name="l00228"></a><span class="lineno"> 228</span>  <span class="keywordflow">if</span> (compute_hash)</div>
<div class="line"><a name="l00229"></a><span class="lineno"> 229</span>  {</div>
<div class="line"><a name="l00230"></a><span class="lineno"> 230</span>  src_file.<a class="code" href="classOpenMS_1_1SourceFile.html#affa32793fdd4f1526a6c34c17626a60a">setChecksum</a>(computeFileHash_(filename), <a class="code" href="classOpenMS_1_1SourceFile.html#a6440df7f4dbfc4c3370e2b6781bc74e5a27028cc8b5d6f0a1cb3030c180019abc">SourceFile::SHA1</a>);</div>
<div class="line"><a name="l00231"></a><span class="lineno"> 231</span>  }</div>
<div class="line"><a name="l00232"></a><span class="lineno"> 232</span> </div>
<div class="line"><a name="l00233"></a><span class="lineno"> 233</span>  exp.<a class="code" href="classOpenMS_1_1ExperimentalSettings.html#a9b357a65e5ec19027b8fa94379439f8c">getSourceFiles</a>().clear();</div>
<div class="line"><a name="l00234"></a><span class="lineno"> 234</span>  exp.<a class="code" href="classOpenMS_1_1ExperimentalSettings.html#a9b357a65e5ec19027b8fa94379439f8c">getSourceFiles</a>().push_back(src_file);</div>
<div class="line"><a name="l00235"></a><span class="lineno"> 235</span> </div>
<div class="line"><a name="l00236"></a><span class="lineno"> 236</span>  <span class="keywordflow">return</span> <span class="keyword">true</span>;</div>
<div class="line"><a name="l00237"></a><span class="lineno"> 237</span>  }</div>
<div class="line"><a name="l00238"></a><span class="lineno"> 238</span> </div>
<div class="line"><a name="l00250"></a><span class="lineno"> 250</span>  <span class="keyword">template</span> <<span class="keyword">class</span> PeakType></div>
<div class="line"><a name="l00251"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FileHandler.html#a4a8354ef45f8a0eac5a5038b3a025f37"> 251</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1FileHandler.html#a4a8354ef45f8a0eac5a5038b3a025f37">storeExperiment</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& filename, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment<PeakType></a>& exp, <a class="code" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87c">ProgressLogger::LogType</a> log = <a class="code" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87cac157bdf0b85a40d2619cbc8bc1ae5fe2">ProgressLogger::NONE</a>)</div>
<div class="line"><a name="l00252"></a><span class="lineno"> 252</span>  {</div>
<div class="line"><a name="l00253"></a><span class="lineno"> 253</span>  <span class="comment">//load right file</span></div>
<div class="line"><a name="l00254"></a><span class="lineno"> 254</span>  <span class="keywordflow">switch</span> (getTypeByFileName(filename))</div>
<div class="line"><a name="l00255"></a><span class="lineno"> 255</span>  {</div>
<div class="line"><a name="l00256"></a><span class="lineno"> 256</span>  <span class="keywordflow">case</span> <a class="code" href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7a66c2f5cd90913752f565186657e85d84">FileTypes::DTA2D</a>:</div>
<div class="line"><a name="l00257"></a><span class="lineno"> 257</span>  {</div>
<div class="line"><a name="l00258"></a><span class="lineno"> 258</span>  <a class="code" href="classOpenMS_1_1DTA2DFile.html">DTA2DFile</a> f;</div>
<div class="line"><a name="l00259"></a><span class="lineno"> 259</span>  f.<a class="code" href="classOpenMS_1_1DTA2DFile.html#a819235ed2844f03df53f4983a7008f28">getOptions</a>() = options_;</div>
<div class="line"><a name="l00260"></a><span class="lineno"> 260</span>  f.<a class="code" href="classOpenMS_1_1ProgressLogger.html#acc3538c5284777d8702ccaefeb61e74c">setLogType</a>(log);</div>
<div class="line"><a name="l00261"></a><span class="lineno"> 261</span>  f.<a class="code" href="classOpenMS_1_1DTA2DFile.html#adb795d215478320be7c6130ff7ddf853">store</a>(filename, exp);</div>
<div class="line"><a name="l00262"></a><span class="lineno"> 262</span>  }</div>
<div class="line"><a name="l00263"></a><span class="lineno"> 263</span>  <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l00264"></a><span class="lineno"> 264</span> </div>
<div class="line"><a name="l00265"></a><span class="lineno"> 265</span>  <span class="keywordflow">case</span> <a class="code" href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7af8a53519bd415aacd429c4239bbfd66e">FileTypes::MZXML</a>:</div>
<div class="line"><a name="l00266"></a><span class="lineno"> 266</span>  {</div>
<div class="line"><a name="l00267"></a><span class="lineno"> 267</span>  <a class="code" href="classOpenMS_1_1MzXMLFile.html">MzXMLFile</a> f;</div>
<div class="line"><a name="l00268"></a><span class="lineno"> 268</span>  f.<a class="code" href="classOpenMS_1_1MzXMLFile.html#a819235ed2844f03df53f4983a7008f28">getOptions</a>() = options_;</div>
<div class="line"><a name="l00269"></a><span class="lineno"> 269</span>  f.<a class="code" href="classOpenMS_1_1ProgressLogger.html#acc3538c5284777d8702ccaefeb61e74c">setLogType</a>(log);</div>
<div class="line"><a name="l00270"></a><span class="lineno"> 270</span>  <span class="keywordflow">if</span> (!exp.<a class="code" href="classOpenMS_1_1MSExperiment.html#a02fccfed86a20f8bd0f6b98c23fadb2e">getChromatograms</a>().empty())</div>
<div class="line"><a name="l00271"></a><span class="lineno"> 271</span>  {</div>
<div class="line"><a name="l00272"></a><span class="lineno"> 272</span>  <a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment<PeakType></a> exp2 = exp;</div>
<div class="line"><a name="l00273"></a><span class="lineno"> 273</span>  <a class="code" href="classOpenMS_1_1ChromatogramTools.html">ChromatogramTools</a>().<a class="code" href="classOpenMS_1_1ChromatogramTools.html#a180cb4974eaf3d4dea0de5326b132951">convertChromatogramsToSpectra</a><<a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment<PeakType></a> >(exp2);</div>
<div class="line"><a name="l00274"></a><span class="lineno"> 274</span>  f.<a class="code" href="classOpenMS_1_1MzXMLFile.html#adb795d215478320be7c6130ff7ddf853">store</a>(filename, exp2);</div>
<div class="line"><a name="l00275"></a><span class="lineno"> 275</span>  }</div>
<div class="line"><a name="l00276"></a><span class="lineno"> 276</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00277"></a><span class="lineno"> 277</span>  {</div>
<div class="line"><a name="l00278"></a><span class="lineno"> 278</span>  f.<a class="code" href="classOpenMS_1_1MzXMLFile.html#adb795d215478320be7c6130ff7ddf853">store</a>(filename, exp);</div>
<div class="line"><a name="l00279"></a><span class="lineno"> 279</span>  }</div>
<div class="line"><a name="l00280"></a><span class="lineno"> 280</span>  }</div>
<div class="line"><a name="l00281"></a><span class="lineno"> 281</span>  <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l00282"></a><span class="lineno"> 282</span> </div>
<div class="line"><a name="l00283"></a><span class="lineno"> 283</span>  <span class="keywordflow">case</span> <a class="code" href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7ae5b2d8f7eb59b2fc050e6bc3c1cba802">FileTypes::MZDATA</a>:</div>
<div class="line"><a name="l00284"></a><span class="lineno"> 284</span>  {</div>
<div class="line"><a name="l00285"></a><span class="lineno"> 285</span>  <a class="code" href="classOpenMS_1_1MzDataFile.html">MzDataFile</a> f;</div>
<div class="line"><a name="l00286"></a><span class="lineno"> 286</span>  f.<a class="code" href="classOpenMS_1_1MzDataFile.html#a819235ed2844f03df53f4983a7008f28">getOptions</a>() = options_;</div>
<div class="line"><a name="l00287"></a><span class="lineno"> 287</span>  f.<a class="code" href="classOpenMS_1_1ProgressLogger.html#acc3538c5284777d8702ccaefeb61e74c">setLogType</a>(log);</div>
<div class="line"><a name="l00288"></a><span class="lineno"> 288</span>  <span class="keywordflow">if</span> (!exp.<a class="code" href="classOpenMS_1_1MSExperiment.html#a02fccfed86a20f8bd0f6b98c23fadb2e">getChromatograms</a>().empty())</div>
<div class="line"><a name="l00289"></a><span class="lineno"> 289</span>  {</div>
<div class="line"><a name="l00290"></a><span class="lineno"> 290</span>  <a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment<PeakType></a> exp2 = exp;</div>
<div class="line"><a name="l00291"></a><span class="lineno"> 291</span>  <a class="code" href="classOpenMS_1_1ChromatogramTools.html">ChromatogramTools</a>().<a class="code" href="classOpenMS_1_1ChromatogramTools.html#a180cb4974eaf3d4dea0de5326b132951">convertChromatogramsToSpectra</a><<a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment<PeakType></a> >(exp2);</div>
<div class="line"><a name="l00292"></a><span class="lineno"> 292</span>  f.<a class="code" href="classOpenMS_1_1MzDataFile.html#adb795d215478320be7c6130ff7ddf853">store</a>(filename, exp2);</div>
<div class="line"><a name="l00293"></a><span class="lineno"> 293</span>  }</div>
<div class="line"><a name="l00294"></a><span class="lineno"> 294</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00295"></a><span class="lineno"> 295</span>  {</div>
<div class="line"><a name="l00296"></a><span class="lineno"> 296</span>  f.<a class="code" href="classOpenMS_1_1MzDataFile.html#adb795d215478320be7c6130ff7ddf853">store</a>(filename, exp);</div>
<div class="line"><a name="l00297"></a><span class="lineno"> 297</span>  }</div>
<div class="line"><a name="l00298"></a><span class="lineno"> 298</span>  }</div>
<div class="line"><a name="l00299"></a><span class="lineno"> 299</span>  <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l00300"></a><span class="lineno"> 300</span> </div>
<div class="line"><a name="l00301"></a><span class="lineno"> 301</span>  <span class="keywordflow">default</span>:</div>
<div class="line"><a name="l00302"></a><span class="lineno"> 302</span>  {</div>
<div class="line"><a name="l00303"></a><span class="lineno"> 303</span>  <a class="code" href="classOpenMS_1_1MzMLFile.html">MzMLFile</a> f;</div>
<div class="line"><a name="l00304"></a><span class="lineno"> 304</span>  f.<a class="code" href="classOpenMS_1_1MzMLFile.html#a819235ed2844f03df53f4983a7008f28">getOptions</a>() = options_;</div>
<div class="line"><a name="l00305"></a><span class="lineno"> 305</span>  f.<a class="code" href="classOpenMS_1_1ProgressLogger.html#acc3538c5284777d8702ccaefeb61e74c">setLogType</a>(log);</div>
<div class="line"><a name="l00306"></a><span class="lineno"> 306</span>  f.<a class="code" href="classOpenMS_1_1MzMLFile.html#adb795d215478320be7c6130ff7ddf853">store</a>(filename, exp);</div>
<div class="line"><a name="l00307"></a><span class="lineno"> 307</span>  }</div>
<div class="line"><a name="l00308"></a><span class="lineno"> 308</span>  <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l00309"></a><span class="lineno"> 309</span>  }</div>
<div class="line"><a name="l00310"></a><span class="lineno"> 310</span>  }</div>
<div class="line"><a name="l00311"></a><span class="lineno"> 311</span> </div>
<div class="line"><a name="l00324"></a><span class="lineno"> 324</span>  <span class="keyword">template</span> <<span class="keyword">class</span> FeatureType></div>
<div class="line"><a name="l00325"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FileHandler.html#a5bc5a0452855c2d30d125261783b55cf"> 325</a></span>  <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1FileHandler.html#a5bc5a0452855c2d30d125261783b55cf">loadFeatures</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& filename, <a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap<FeatureType></a>& map, <a class="code" href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7">FileTypes::Type</a> force_type = <a class="code" href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7a6ce26a62afab55d7606ad4e92428b30c">FileTypes::UNKNOWN</a>)</div>
<div class="line"><a name="l00326"></a><span class="lineno"> 326</span>  {</div>
<div class="line"><a name="l00327"></a><span class="lineno"> 327</span>  <span class="comment">//determine file type</span></div>
<div class="line"><a name="l00328"></a><span class="lineno"> 328</span>  <a class="code" href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7">FileTypes::Type</a> type;</div>
<div class="line"><a name="l00329"></a><span class="lineno"> 329</span>  <span class="keywordflow">if</span> (force_type != <a class="code" href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7a6ce26a62afab55d7606ad4e92428b30c">FileTypes::UNKNOWN</a>)</div>
<div class="line"><a name="l00330"></a><span class="lineno"> 330</span>  {</div>
<div class="line"><a name="l00331"></a><span class="lineno"> 331</span>  type = force_type;</div>
<div class="line"><a name="l00332"></a><span class="lineno"> 332</span>  }</div>
<div class="line"><a name="l00333"></a><span class="lineno"> 333</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00334"></a><span class="lineno"> 334</span>  {</div>
<div class="line"><a name="l00335"></a><span class="lineno"> 335</span>  <span class="keywordflow">try</span></div>
<div class="line"><a name="l00336"></a><span class="lineno"> 336</span>  {</div>
<div class="line"><a name="l00337"></a><span class="lineno"> 337</span>  type = getType(filename);</div>
<div class="line"><a name="l00338"></a><span class="lineno"> 338</span>  }</div>
<div class="line"><a name="l00339"></a><span class="lineno"> 339</span>  <span class="keywordflow">catch</span> (<a class="code" href="classOpenMS_1_1Exception_1_1FileNotFound.html">Exception::FileNotFound</a>)</div>
<div class="line"><a name="l00340"></a><span class="lineno"> 340</span>  {</div>
<div class="line"><a name="l00341"></a><span class="lineno"> 341</span>  <span class="keywordflow">return</span> <span class="keyword">false</span>;</div>
<div class="line"><a name="l00342"></a><span class="lineno"> 342</span>  }</div>
<div class="line"><a name="l00343"></a><span class="lineno"> 343</span>  }</div>
<div class="line"><a name="l00344"></a><span class="lineno"> 344</span> </div>
<div class="line"><a name="l00345"></a><span class="lineno"> 345</span>  <span class="comment">//load right file</span></div>
<div class="line"><a name="l00346"></a><span class="lineno"> 346</span>  <span class="keywordflow">if</span> (type == <a class="code" href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7a753b825a63c99787d10e05f7d65a87a6">FileTypes::FEATUREXML</a>)</div>
<div class="line"><a name="l00347"></a><span class="lineno"> 347</span>  {</div>
<div class="line"><a name="l00348"></a><span class="lineno"> 348</span>  <a class="code" href="classOpenMS_1_1FeatureXMLFile.html">FeatureXMLFile</a>().<a class="code" href="classOpenMS_1_1FeatureXMLFile.html#a7315500f55fb5cae883f0b1f2024c5b7">load</a>(filename, map);</div>
<div class="line"><a name="l00349"></a><span class="lineno"> 349</span>  }</div>
<div class="line"><a name="l00350"></a><span class="lineno"> 350</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (type == <a class="code" href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7a9ceeac5c1982a8aeeb7518cb4a488935">FileTypes::TSV</a>)</div>
<div class="line"><a name="l00351"></a><span class="lineno"> 351</span>  {</div>
<div class="line"><a name="l00352"></a><span class="lineno"> 352</span>  <a class="code" href="classOpenMS_1_1MsInspectFile.html">MsInspectFile</a>().<a class="code" href="classOpenMS_1_1MsInspectFile.html#aa4e73ca60efa3ca29e203f46b5187c6c">load</a>(filename, map);</div>
<div class="line"><a name="l00353"></a><span class="lineno"> 353</span>  }</div>
<div class="line"><a name="l00354"></a><span class="lineno"> 354</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (type == <a class="code" href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7a87ac627b0f0c019e05a735e1a00b861d">FileTypes::PEPLIST</a>)</div>
<div class="line"><a name="l00355"></a><span class="lineno"> 355</span>  {</div>
<div class="line"><a name="l00356"></a><span class="lineno"> 356</span>  <a class="code" href="classOpenMS_1_1SpecArrayFile.html">SpecArrayFile</a>().<a class="code" href="classOpenMS_1_1SpecArrayFile.html#aa4e73ca60efa3ca29e203f46b5187c6c">load</a>(filename, map);</div>
<div class="line"><a name="l00357"></a><span class="lineno"> 357</span>  }</div>
<div class="line"><a name="l00358"></a><span class="lineno"> 358</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (type == <a class="code" href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7a55c4004ffd908d6e6ec96028e90916d0">FileTypes::KROENIK</a>)</div>
<div class="line"><a name="l00359"></a><span class="lineno"> 359</span>  {</div>
<div class="line"><a name="l00360"></a><span class="lineno"> 360</span>  <a class="code" href="classOpenMS_1_1KroenikFile.html">KroenikFile</a>().<a class="code" href="classOpenMS_1_1KroenikFile.html#aa4e73ca60efa3ca29e203f46b5187c6c">load</a>(filename, map);</div>
<div class="line"><a name="l00361"></a><span class="lineno"> 361</span>  }</div>
<div class="line"><a name="l00362"></a><span class="lineno"> 362</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00363"></a><span class="lineno"> 363</span>  {</div>
<div class="line"><a name="l00364"></a><span class="lineno"> 364</span>  <span class="keywordflow">return</span> <span class="keyword">false</span>;</div>
<div class="line"><a name="l00365"></a><span class="lineno"> 365</span>  }</div>
<div class="line"><a name="l00366"></a><span class="lineno"> 366</span> </div>
<div class="line"><a name="l00367"></a><span class="lineno"> 367</span>  <span class="keywordflow">return</span> <span class="keyword">true</span>;</div>
<div class="line"><a name="l00368"></a><span class="lineno"> 368</span>  }</div>
<div class="line"><a name="l00369"></a><span class="lineno"> 369</span> </div>
<div class="line"><a name="l00370"></a><span class="lineno"> 370</span> <span class="keyword">private</span>:</div>
<div class="line"><a name="l00371"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FileHandler.html#a654a0b5941d937e303c64bc9e732baec"> 371</a></span>  <a class="code" href="classOpenMS_1_1PeakFileOptions.html">PeakFileOptions</a> <a class="code" href="classOpenMS_1_1FileHandler.html#a654a0b5941d937e303c64bc9e732baec">options_</a>;</div>
<div class="line"><a name="l00372"></a><span class="lineno"> 372</span> </div>
<div class="line"><a name="l00378"></a><span class="lineno"> 378</span>  <a class="code" href="classOpenMS_1_1String.html">String</a> computeFileHash_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& filename) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00379"></a><span class="lineno"> 379</span>  };</div>
<div class="line"><a name="l00380"></a><span class="lineno"> 380</span> </div>
<div class="line"><a name="l00381"></a><span class="lineno"> 381</span> } <span class="comment">//namespace</span></div>
<div class="line"><a name="l00382"></a><span class="lineno"> 382</span> </div>
<div class="line"><a name="l00383"></a><span class="lineno"> 383</span> <span class="preprocessor">#endif //OPENMS_FORMAT_FILEHANDLER_H</span></div>
<div class="ttc" id="structOpenMS_1_1FileTypes_html_a1d1cfd8ffb84e947f82999c682b666a7"><div class="ttname"><a href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7">OpenMS::FileTypes::Type</a></div><div class="ttdeci">Type</div><div class="ttdoc">Actual file types enum. </div><div class="ttdef"><b>Definition:</b> FileTypes.h:59</div></div>
<div class="ttc" id="classOpenMS_1_1DTA2DFile_html"><div class="ttname"><a href="classOpenMS_1_1DTA2DFile.html">OpenMS::DTA2DFile</a></div><div class="ttdoc">DTA2D File adapter. </div><div class="ttdef"><b>Definition:</b> DTA2DFile.h:64</div></div>
<div class="ttc" id="structOpenMS_1_1FileTypes_html_a1d1cfd8ffb84e947f82999c682b666a7a9ceeac5c1982a8aeeb7518cb4a488935"><div class="ttname"><a href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7a9ceeac5c1982a8aeeb7518cb4a488935">OpenMS::FileTypes::TSV</a></div><div class="ttdoc">msInspect file (.tsv) </div><div class="ttdef"><b>Definition:</b> FileTypes.h:87</div></div>
<div class="ttc" id="classOpenMS_1_1FileHandler_html_a654a0b5941d937e303c64bc9e732baec"><div class="ttname"><a href="classOpenMS_1_1FileHandler.html#a654a0b5941d937e303c64bc9e732baec">OpenMS::FileHandler::options_</a></div><div class="ttdeci">PeakFileOptions options_</div><div class="ttdef"><b>Definition:</b> FileHandler.h:371</div></div>
<div class="ttc" id="classOpenMS_1_1XMassFile_html_a865164e026ef00fa12377c1d63613613"><div class="ttname"><a href="classOpenMS_1_1XMassFile.html#a865164e026ef00fa12377c1d63613613">OpenMS::XMassFile::load</a></div><div class="ttdeci">void load(const String &filename, MSSpectrum< PeakType > &spectrum)</div><div class="ttdoc">Loads a spectrum from a XMass file. </div><div class="ttdef"><b>Definition:</b> XMassFile.h:84</div></div>
<div class="ttc" id="classOpenMS_1_1MzXMLFile_html_adb795d215478320be7c6130ff7ddf853"><div class="ttname"><a href="classOpenMS_1_1MzXMLFile.html#adb795d215478320be7c6130ff7ddf853">OpenMS::MzXMLFile::store</a></div><div class="ttdeci">void store(const String &filename, const MapType &map) const </div><div class="ttdoc">Stores a map in a MzXML file. </div><div class="ttdef"><b>Definition:</b> MzXMLFile.h:101</div></div>
<div class="ttc" id="FeatureXMLFile_8h_html"><div class="ttname"><a href="FeatureXMLFile_8h.html">FeatureXMLFile.h</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="structOpenMS_1_1FileTypes_html_a1d1cfd8ffb84e947f82999c682b666a7ac59ebe001fb1923baf25b050436a5f15"><div class="ttname"><a href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7ac59ebe001fb1923baf25b050436a5f15">OpenMS::FileTypes::MS2</a></div><div class="ttdoc">MS2 file (.ms2) </div><div class="ttdef"><b>Definition:</b> FileTypes.h:74</div></div>
<div class="ttc" id="classOpenMS_1_1MzXMLFile_html"><div class="ttname"><a href="classOpenMS_1_1MzXMLFile.html">OpenMS::MzXMLFile</a></div><div class="ttdoc">File adapter for MzXML 2.1 files. </div><div class="ttdef"><b>Definition:</b> MzXMLFile.h:52</div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html_ad20897c5c8bd47f5d4005989bead0e55"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html#ad20897c5c8bd47f5d4005989bead0e55">OpenMS::MSExperiment::reset</a></div><div class="ttdeci">void reset()</div><div class="ttdoc">Resets all internal values. </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:635</div></div>
<div class="ttc" id="classOpenMS_1_1ProgressLogger_html_af67907baa897e9fb84df0cb89795b87c"><div class="ttname"><a href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87c">OpenMS::ProgressLogger::LogType</a></div><div class="ttdeci">LogType</div><div class="ttdoc">Possible log types. </div><div class="ttdef"><b>Definition:</b> ProgressLogger.h:66</div></div>
<div class="ttc" id="classOpenMS_1_1MsInspectFile_html_aa4e73ca60efa3ca29e203f46b5187c6c"><div class="ttname"><a href="classOpenMS_1_1MsInspectFile.html#aa4e73ca60efa3ca29e203f46b5187c6c">OpenMS::MsInspectFile::load</a></div><div class="ttdeci">void load(const String &filename, FeatureMapType &feature_map)</div><div class="ttdoc">Loads a MsInspect file into a featureXML. </div><div class="ttdef"><b>Definition:</b> MsInspectFile.h:78</div></div>
<div class="ttc" id="classOpenMS_1_1ChromatogramTools_html_a180cb4974eaf3d4dea0de5326b132951"><div class="ttname"><a href="classOpenMS_1_1ChromatogramTools.html#a180cb4974eaf3d4dea0de5326b132951">OpenMS::ChromatogramTools::convertChromatogramsToSpectra</a></div><div class="ttdeci">void convertChromatogramsToSpectra(ExperimentType &exp)</div><div class="ttdoc">converts the chromatogram to a list of spectra with instrument settings SRM </div><div class="ttdef"><b>Definition:</b> ChromatogramTools.h:86</div></div>
<div class="ttc" id="classOpenMS_1_1MzXMLFile_html_aed378b9a389ec00fa2b559bf7d3b710b"><div class="ttname"><a href="classOpenMS_1_1MzXMLFile.html#aed378b9a389ec00fa2b559bf7d3b710b">OpenMS::MzXMLFile::load</a></div><div class="ttdeci">void load(const String &filename, MapType &map)</div><div class="ttdoc">Loads a map from a MzXML file. </div><div class="ttdef"><b>Definition:</b> MzXMLFile.h:80</div></div>
<div class="ttc" id="XMassFile_8h_html"><div class="ttname"><a href="XMassFile_8h.html">XMassFile.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1FeatureMap_html"><div class="ttname"><a href="classOpenMS_1_1FeatureMap.html">OpenMS::FeatureMap</a></div><div class="ttdoc">A container for features. </div><div class="ttdef"><b>Definition:</b> FeatureMap.h:111</div></div>
<div class="ttc" id="ProgressLogger_8h_html"><div class="ttname"><a href="ProgressLogger_8h.html">ProgressLogger.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1File_html_a43bdcb2e5cb18da64e25b2467c8fdcaa"><div class="ttname"><a href="classOpenMS_1_1File.html#a43bdcb2e5cb18da64e25b2467c8fdcaa">OpenMS::File::path</a></div><div class="ttdeci">static String path(const String &file)</div><div class="ttdoc">Returns the path of the file (without the file name). </div></div>
<div class="ttc" id="classOpenMS_1_1SourceFile_html_a2d47bfad02d5ce05dcfab38bc1b21400"><div class="ttname"><a href="classOpenMS_1_1SourceFile.html#a2d47bfad02d5ce05dcfab38bc1b21400">OpenMS::SourceFile::setFileType</a></div><div class="ttdeci">void setFileType(const String &file_type)</div><div class="ttdoc">sets the file type </div></div>
<div class="ttc" id="classOpenMS_1_1FileHandler_html_a5bc5a0452855c2d30d125261783b55cf"><div class="ttname"><a href="classOpenMS_1_1FileHandler.html#a5bc5a0452855c2d30d125261783b55cf">OpenMS::FileHandler::loadFeatures</a></div><div class="ttdeci">bool loadFeatures(const String &filename, FeatureMap< FeatureType > &map, FileTypes::Type force_type=FileTypes::UNKNOWN)</div><div class="ttdoc">Loads a file into a FeatureMap. </div><div class="ttdef"><b>Definition:</b> FileHandler.h:325</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="structOpenMS_1_1FileTypes_html_a1d1cfd8ffb84e947f82999c682b666a7ae5b2d8f7eb59b2fc050e6bc3c1cba802"><div class="ttname"><a href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7ae5b2d8f7eb59b2fc050e6bc3c1cba802">OpenMS::FileTypes::MZDATA</a></div><div class="ttdoc">MzData file (.mzData) </div><div class="ttdef"><b>Definition:</b> FileTypes.h:64</div></div>
<div class="ttc" id="classOpenMS_1_1SourceFile_html"><div class="ttname"><a href="classOpenMS_1_1SourceFile.html">OpenMS::SourceFile</a></div><div class="ttdoc">Description of a file location, used to store the origin of (meta) data. </div><div class="ttdef"><b>Definition:</b> SourceFile.h:47</div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html_ac2bc824d6ff2633ec34793c9e918d479"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html#ac2bc824d6ff2633ec34793c9e918d479">OpenMS::MSExperiment::resize</a></div><div class="ttdeci">void resize(Size s)</div><div class="ttdef"><b>Definition:</b> MSExperiment.h:122</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_1XMassFile_html"><div class="ttname"><a href="classOpenMS_1_1XMassFile.html">OpenMS::XMassFile</a></div><div class="ttdoc">File adapter for &#39;XMass Analysis (fid)&#39; files. </div><div class="ttdef"><b>Definition:</b> XMassFile.h:66</div></div>
<div class="ttc" id="MS2File_8h_html"><div class="ttname"><a href="MS2File_8h.html">MS2File.h</a></div></div>
<div class="ttc" id="DTA2DFile_8h_html"><div class="ttname"><a href="DTA2DFile_8h.html">DTA2DFile.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1KroenikFile_html"><div class="ttname"><a href="classOpenMS_1_1KroenikFile.html">OpenMS::KroenikFile</a></div><div class="ttdoc">File adapter for Kroenik (HardKloer sibling) files. </div><div class="ttdef"><b>Definition:</b> KroenikFile.h:67</div></div>
<div class="ttc" id="classOpenMS_1_1SourceFile_html_affa32793fdd4f1526a6c34c17626a60a"><div class="ttname"><a href="classOpenMS_1_1SourceFile.html#affa32793fdd4f1526a6c34c17626a60a">OpenMS::SourceFile::setChecksum</a></div><div class="ttdeci">void setChecksum(const String &checksum, ChecksumType type)</div><div class="ttdoc">sets the file&#39;s checksum </div></div>
<div class="ttc" id="classOpenMS_1_1MascotGenericFile_html"><div class="ttname"><a href="classOpenMS_1_1MascotGenericFile.html">OpenMS::MascotGenericFile</a></div><div class="ttdoc">Mascot input file adapter. </div><div class="ttdef"><b>Definition:</b> MascotGenericFile.h:64</div></div>
<div class="ttc" id="MzDataFile_8h_html"><div class="ttname"><a href="MzDataFile_8h.html">MzDataFile.h</a></div></div>
<div class="ttc" id="structOpenMS_1_1FileTypes_html_a1d1cfd8ffb84e947f82999c682b666a7a87ac627b0f0c019e05a735e1a00b861d"><div class="ttname"><a href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7a87ac627b0f0c019e05a735e1a00b861d">OpenMS::FileTypes::PEPLIST</a></div><div class="ttdoc">specArray file (.peplist) </div><div class="ttdef"><b>Definition:</b> FileTypes.h:88</div></div>
<div class="ttc" id="classOpenMS_1_1SpecArrayFile_html"><div class="ttname"><a href="classOpenMS_1_1SpecArrayFile.html">OpenMS::SpecArrayFile</a></div><div class="ttdoc">File adapter for SpecArray (.pepList) files. </div><div class="ttdef"><b>Definition:</b> SpecArrayFile.h:61</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureXMLFile_html_a7315500f55fb5cae883f0b1f2024c5b7"><div class="ttname"><a href="classOpenMS_1_1FeatureXMLFile.html#a7315500f55fb5cae883f0b1f2024c5b7">OpenMS::FeatureXMLFile::load</a></div><div class="ttdeci">void load(const String &filename, FeatureMap<> &feature_map)</div><div class="ttdoc">loads the file with name filename into map and calls updateRanges(). </div></div>
<div class="ttc" id="classOpenMS_1_1MzMLFile_html"><div class="ttname"><a href="classOpenMS_1_1MzMLFile.html">OpenMS::MzMLFile</a></div><div class="ttdoc">File adapter for MzML files. </div><div class="ttdef"><b>Definition:</b> MzMLFile.h:58</div></div>
<div class="ttc" id="MzXMLFile_8h_html"><div class="ttname"><a href="MzXMLFile_8h.html">MzXMLFile.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 &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>
<div class="ttc" id="structOpenMS_1_1FileTypes_html_a1d1cfd8ffb84e947f82999c682b666a7a6ce26a62afab55d7606ad4e92428b30c"><div class="ttname"><a href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7a6ce26a62afab55d7606ad4e92428b30c">OpenMS::FileTypes::UNKNOWN</a></div><div class="ttdoc">Unknown file extension. </div><div class="ttdef"><b>Definition:</b> FileTypes.h:61</div></div>
<div class="ttc" id="classOpenMS_1_1MzDataFile_html"><div class="ttname"><a href="classOpenMS_1_1MzDataFile.html">OpenMS::MzDataFile</a></div><div class="ttdoc">File adapter for MzData files. </div><div class="ttdef"><b>Definition:</b> MzDataFile.h:51</div></div>
<div class="ttc" id="classOpenMS_1_1ProgressLogger_html_af67907baa897e9fb84df0cb89795b87cac157bdf0b85a40d2619cbc8bc1ae5fe2"><div class="ttname"><a href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87cac157bdf0b85a40d2619cbc8bc1ae5fe2">OpenMS::ProgressLogger::NONE</a></div><div class="ttdoc">No progress logging. </div><div class="ttdef"><b>Definition:</b> ProgressLogger.h:70</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 &filename, MapType &exp)</div><div class="ttdef"><b>Definition:</b> MS2File.h:77</div></div>
<div class="ttc" id="structOpenMS_1_1FileTypes_html_a1d1cfd8ffb84e947f82999c682b666a7ad8654d9b2a9c38ece897bfbdd8152214"><div class="ttname"><a href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7ad8654d9b2a9c38ece897bfbdd8152214">OpenMS::FileTypes::DTA</a></div><div class="ttdoc">DTA file (.dta) </div><div class="ttdef"><b>Definition:</b> FileTypes.h:62</div></div>
<div class="ttc" id="structOpenMS_1_1FileTypes_html_a1d1cfd8ffb84e947f82999c682b666a7a87b48e9729223183349bdfb171076285"><div class="ttname"><a href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7a87b48e9729223183349bdfb171076285">OpenMS::FileTypes::XMASS</a></div><div class="ttdoc">XMass Analysis file (fid) </div><div class="ttdef"><b>Definition:</b> FileTypes.h:86</div></div>
<div class="ttc" id="SpecArrayFile_8h_html"><div class="ttname"><a href="SpecArrayFile_8h.html">SpecArrayFile.h</a></div></div>
<div class="ttc" id="structOpenMS_1_1FileTypes_html_a1d1cfd8ffb84e947f82999c682b666a7a55c4004ffd908d6e6ec96028e90916d0"><div class="ttname"><a href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7a55c4004ffd908d6e6ec96028e90916d0">OpenMS::FileTypes::KROENIK</a></div><div class="ttdoc">kroenik file (.kroenik) </div><div class="ttdef"><b>Definition:</b> FileTypes.h:90</div></div>
<div class="ttc" id="classOpenMS_1_1MzMLFile_html_aed378b9a389ec00fa2b559bf7d3b710b"><div class="ttname"><a href="classOpenMS_1_1MzMLFile.html#aed378b9a389ec00fa2b559bf7d3b710b">OpenMS::MzMLFile::load</a></div><div class="ttdeci">void load(const String &filename, MapType &map)</div><div class="ttdoc">Loads a map from a MzML file. </div><div class="ttdef"><b>Definition:</b> MzMLFile.h:86</div></div>
<div class="ttc" id="classOpenMS_1_1MzMLFile_html_adb795d215478320be7c6130ff7ddf853"><div class="ttname"><a href="classOpenMS_1_1MzMLFile.html#adb795d215478320be7c6130ff7ddf853">OpenMS::MzMLFile::store</a></div><div class="ttdeci">void store(const String &filename, const MapType &map) const </div><div class="ttdoc">Stores a map in a MzML file. </div><div class="ttdef"><b>Definition:</b> MzMLFile.h:126</div></div>
<div class="ttc" id="classOpenMS_1_1DTA2DFile_html_adb795d215478320be7c6130ff7ddf853"><div class="ttname"><a href="classOpenMS_1_1DTA2DFile.html#adb795d215478320be7c6130ff7ddf853">OpenMS::DTA2DFile::store</a></div><div class="ttdeci">void store(const String &filename, const MapType &map) const </div><div class="ttdoc">Stores a map in a DTA2D file. </div><div class="ttdef"><b>Definition:</b> DTA2DFile.h:268</div></div>
<div class="ttc" id="classOpenMS_1_1MzDataFile_html_adb795d215478320be7c6130ff7ddf853"><div class="ttname"><a href="classOpenMS_1_1MzDataFile.html#adb795d215478320be7c6130ff7ddf853">OpenMS::MzDataFile::store</a></div><div class="ttdeci">void store(const String &filename, const MapType &map) const </div><div class="ttdoc">Stores a map in a MzData file. </div><div class="ttdef"><b>Definition:</b> MzDataFile.h:102</div></div>
<div class="ttc" id="classOpenMS_1_1ChromatogramTools_html_af3ff28dcfb8f80c33a57605672ebb0b1"><div class="ttname"><a href="classOpenMS_1_1ChromatogramTools.html#af3ff28dcfb8f80c33a57605672ebb0b1">OpenMS::ChromatogramTools::convertSpectraToChromatograms</a></div><div class="ttdeci">void convertSpectraToChromatograms(ExperimentType &exp, bool remove_spectra=false)</div><div class="ttdoc">converts e.g. SRM spectra to chromatograms </div><div class="ttdef"><b>Definition:</b> ChromatogramTools.h:138</div></div>
<div class="ttc" id="DTAFile_8h_html"><div class="ttname"><a href="DTAFile_8h.html">DTAFile.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1SourceFile_html_af0a7eddbacf20c4f4045b671df6b0fe7"><div class="ttname"><a href="classOpenMS_1_1SourceFile.html#af0a7eddbacf20c4f4045b671df6b0fe7">OpenMS::SourceFile::setNameOfFile</a></div><div class="ttdeci">void setNameOfFile(const String &name_of_file)</div><div class="ttdoc">sets the file name </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 &file)</div><div class="ttdoc">Returns the basename of the file (without the path). </div></div>
<div class="ttc" id="structOpenMS_1_1FileTypes_html_a1d1cfd8ffb84e947f82999c682b666a7a753b825a63c99787d10e05f7d65a87a6"><div class="ttname"><a href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7a753b825a63c99787d10e05f7d65a87a6">OpenMS::FileTypes::FEATUREXML</a></div><div class="ttdoc">OpenMS feature file (.featureXML) </div><div class="ttdef"><b>Definition:</b> FileTypes.h:66</div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html">OpenMS::MSExperiment</a></div><div class="ttdoc">Representation of a mass spectrometry experiment. </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:68</div></div>
<div class="ttc" id="classOpenMS_1_1SourceFile_html_a6440df7f4dbfc4c3370e2b6781bc74e5a27028cc8b5d6f0a1cb3030c180019abc"><div class="ttname"><a href="classOpenMS_1_1SourceFile.html#a6440df7f4dbfc4c3370e2b6781bc74e5a27028cc8b5d6f0a1cb3030c180019abc">OpenMS::SourceFile::SHA1</a></div><div class="ttdoc">Secure Hash Algorithm-1. </div><div class="ttdef"><b>Definition:</b> SourceFile.h:55</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureXMLFile_html"><div class="ttname"><a href="classOpenMS_1_1FeatureXMLFile.html">OpenMS::FeatureXMLFile</a></div><div class="ttdoc">This class provides Input/Output functionality for feature maps. </div><div class="ttdef"><b>Definition:</b> FeatureXMLFile.h:59</div></div>
<div class="ttc" id="classOpenMS_1_1DTA2DFile_html_a819235ed2844f03df53f4983a7008f28"><div class="ttname"><a href="classOpenMS_1_1DTA2DFile.html#a819235ed2844f03df53f4983a7008f28">OpenMS::DTA2DFile::getOptions</a></div><div class="ttdeci">PeakFileOptions & getOptions()</div><div class="ttdoc">Mutable access to the options for loading/storing. </div></div>
<div class="ttc" id="MascotGenericFile_8h_html"><div class="ttname"><a href="MascotGenericFile_8h.html">MascotGenericFile.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1MzDataFile_html_a819235ed2844f03df53f4983a7008f28"><div class="ttname"><a href="classOpenMS_1_1MzDataFile.html#a819235ed2844f03df53f4983a7008f28">OpenMS::MzDataFile::getOptions</a></div><div class="ttdeci">PeakFileOptions & getOptions()</div><div class="ttdoc">Mutable access to the options for loading/storing. </div></div>
<div class="ttc" id="classOpenMS_1_1MzMLFile_html_a819235ed2844f03df53f4983a7008f28"><div class="ttname"><a href="classOpenMS_1_1MzMLFile.html#a819235ed2844f03df53f4983a7008f28">OpenMS::MzMLFile::getOptions</a></div><div class="ttdeci">PeakFileOptions & getOptions()</div><div class="ttdoc">Mutable access to the options for loading/storing. </div></div>
<div class="ttc" id="classOpenMS_1_1FileHandler_html_a4a8354ef45f8a0eac5a5038b3a025f37"><div class="ttname"><a href="classOpenMS_1_1FileHandler.html#a4a8354ef45f8a0eac5a5038b3a025f37">OpenMS::FileHandler::storeExperiment</a></div><div class="ttdeci">void storeExperiment(const String &filename, const MSExperiment< PeakType > &exp, ProgressLogger::LogType log=ProgressLogger::NONE)</div><div class="ttdoc">Stores an MSExperiment to a file. </div><div class="ttdef"><b>Definition:</b> FileHandler.h:251</div></div>
<div class="ttc" id="classOpenMS_1_1FileHandler_html_a408091416e0e1f6019abd59bdb6a9269"><div class="ttname"><a href="classOpenMS_1_1FileHandler.html#a408091416e0e1f6019abd59bdb6a9269">OpenMS::FileHandler::loadExperiment</a></div><div class="ttdeci">bool loadExperiment(const String &filename, MSExperiment< PeakType > &exp, FileTypes::Type force_type=FileTypes::UNKNOWN, ProgressLogger::LogType log=ProgressLogger::NONE, const bool compute_hash=true)</div><div class="ttdoc">Loads a file into an MSExperiment. </div><div class="ttdef"><b>Definition:</b> FileHandler.h:121</div></div>
<div class="ttc" id="structOpenMS_1_1FileTypes_html_a854df315fb804a3fba0232334a7f1d0f"><div class="ttname"><a href="structOpenMS_1_1FileTypes.html#a854df315fb804a3fba0232334a7f1d0f">OpenMS::FileTypes::typeToMZML</a></div><div class="ttdeci">static String typeToMZML(Type type)</div><div class="ttdoc">Returns the mzML name (TODO: switch to accession since they are more stable!) </div></div>
<div class="ttc" id="structOpenMS_1_1FileTypes_html_a1d1cfd8ffb84e947f82999c682b666a7a66c2f5cd90913752f565186657e85d84"><div class="ttname"><a href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7a66c2f5cd90913752f565186657e85d84">OpenMS::FileTypes::DTA2D</a></div><div class="ttdoc">DTA2D file (.dta2d) </div><div class="ttdef"><b>Definition:</b> FileTypes.h:63</div></div>
<div class="ttc" id="classOpenMS_1_1XMassFile_html_a43556a513eaa5395c068a7c9874cc6d1"><div class="ttname"><a href="classOpenMS_1_1XMassFile.html#a43556a513eaa5395c068a7c9874cc6d1">OpenMS::XMassFile::importExperimentalSettings</a></div><div class="ttdeci">void importExperimentalSettings(const String &filename, MSExperiment< PeakType > &exp)</div><div class="ttdoc">Import settings from a XMass file. </div><div class="ttdef"><b>Definition:</b> XMassFile.h:182</div></div>
<div class="ttc" id="classOpenMS_1_1SpecArrayFile_html_aa4e73ca60efa3ca29e203f46b5187c6c"><div class="ttname"><a href="classOpenMS_1_1SpecArrayFile.html#aa4e73ca60efa3ca29e203f46b5187c6c">OpenMS::SpecArrayFile::load</a></div><div class="ttdeci">void load(const String &filename, FeatureMapType &feature_map)</div><div class="ttdoc">Loads a SpecArray file into a featureXML. </div><div class="ttdef"><b>Definition:</b> SpecArrayFile.h:78</div></div>
<div class="ttc" id="classOpenMS_1_1ChromatogramTools_html"><div class="ttname"><a href="classOpenMS_1_1ChromatogramTools.html">OpenMS::ChromatogramTools</a></div><div class="ttdoc">Conversion class to interconvert chromatograms. </div><div class="ttdef"><b>Definition:</b> ChromatogramTools.h:55</div></div>
<div class="ttc" id="classOpenMS_1_1PeakFileOptions_html"><div class="ttname"><a href="classOpenMS_1_1PeakFileOptions.html">OpenMS::PeakFileOptions</a></div><div class="ttdoc">Options for loading files containing peak data. </div><div class="ttdef"><b>Definition:</b> PeakFileOptions.h:47</div></div>
<div class="ttc" id="classOpenMS_1_1MsInspectFile_html"><div class="ttname"><a href="classOpenMS_1_1MsInspectFile.html">OpenMS::MsInspectFile</a></div><div class="ttdoc">File adapter for MsInspect files. </div><div class="ttdef"><b>Definition:</b> MsInspectFile.h:61</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="classOpenMS_1_1MascotGenericFile_html_a98bebe67b8b06a9a67a3654d631355b4"><div class="ttname"><a href="classOpenMS_1_1MascotGenericFile.html#a98bebe67b8b06a9a67a3654d631355b4">OpenMS::MascotGenericFile::load</a></div><div class="ttdeci">void load(const String &filename, MapType &exp)</div><div class="ttdoc">loads a Mascot Generic File into a PeakMap </div><div class="ttdef"><b>Definition:</b> MascotGenericFile.h:90</div></div>
<div class="ttc" id="classOpenMS_1_1SourceFile_html_a2edd9a092842480801a9738a3a514fb3"><div class="ttname"><a href="classOpenMS_1_1SourceFile.html#a2edd9a092842480801a9738a3a514fb3">OpenMS::SourceFile::setPathToFile</a></div><div class="ttdeci">void setPathToFile(const String &path_path_to_file)</div><div class="ttdoc">sets the file path </div></div>
<div class="ttc" id="classOpenMS_1_1MzXMLFile_html_a819235ed2844f03df53f4983a7008f28"><div class="ttname"><a href="classOpenMS_1_1MzXMLFile.html#a819235ed2844f03df53f4983a7008f28">OpenMS::MzXMLFile::getOptions</a></div><div class="ttdeci">PeakFileOptions & getOptions()</div><div class="ttdoc">Mutable access to the options for loading/storing. </div></div>
<div class="ttc" id="structOpenMS_1_1FileTypes_html_a1d1cfd8ffb84e947f82999c682b666a7a29bb13323f25136faf82e418da451b26"><div class="ttname"><a href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7a29bb13323f25136faf82e418da451b26">OpenMS::FileTypes::MGF</a></div><div class="ttdoc">Mascot Generic Format (.mgf) </div><div class="ttdef"><b>Definition:</b> FileTypes.h:69</div></div>
<div class="ttc" id="classOpenMS_1_1KroenikFile_html_aa4e73ca60efa3ca29e203f46b5187c6c"><div class="ttname"><a href="classOpenMS_1_1KroenikFile.html#aa4e73ca60efa3ca29e203f46b5187c6c">OpenMS::KroenikFile::load</a></div><div class="ttdeci">void load(const String &filename, FeatureMapType &feature_map)</div><div class="ttdoc">Loads a Kroenik file into a featureXML. </div><div class="ttdef"><b>Definition:</b> KroenikFile.h:84</div></div>
<div class="ttc" id="ChromatogramTools_8h_html"><div class="ttname"><a href="ChromatogramTools_8h.html">ChromatogramTools.h</a></div></div>
<div class="ttc" id="FileTypes_8h_html"><div class="ttname"><a href="FileTypes_8h.html">FileTypes.h</a></div></div>
<div class="ttc" id="MsInspectFile_8h_html"><div class="ttname"><a href="MsInspectFile_8h.html">MsInspectFile.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1MzDataFile_html_aed378b9a389ec00fa2b559bf7d3b710b"><div class="ttname"><a href="classOpenMS_1_1MzDataFile.html#aed378b9a389ec00fa2b559bf7d3b710b">OpenMS::MzDataFile::load</a></div><div class="ttdeci">void load(const String &filename, MapType &map)</div><div class="ttdoc">Loads a map from a MzData file. </div><div class="ttdef"><b>Definition:</b> MzDataFile.h:81</div></div>
<div class="ttc" id="MzMLFile_8h_html"><div class="ttname"><a href="MzMLFile_8h.html">MzMLFile.h</a></div></div>
<div class="ttc" id="structOpenMS_1_1FileTypes_html_a1d1cfd8ffb84e947f82999c682b666a7ab5518cc16bd1f60ebbb47e681a56b75f"><div class="ttname"><a href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7ab5518cc16bd1f60ebbb47e681a56b75f">OpenMS::FileTypes::MZML</a></div><div class="ttdoc">MzML file (.mzML) </div><div class="ttdef"><b>Definition:</b> FileTypes.h:73</div></div>
<div class="ttc" id="classOpenMS_1_1FileHandler_html"><div class="ttname"><a href="classOpenMS_1_1FileHandler.html">OpenMS::FileHandler</a></div><div class="ttdoc">Facilitates file handling by file type recognition. </div><div class="ttdef"><b>Definition:</b> FileHandler.h:73</div></div>
<div class="ttc" id="classOpenMS_1_1DTA2DFile_html_aed378b9a389ec00fa2b559bf7d3b710b"><div class="ttname"><a href="classOpenMS_1_1DTA2DFile.html#aed378b9a389ec00fa2b559bf7d3b710b">OpenMS::DTA2DFile::load</a></div><div class="ttdeci">void load(const String &filename, MapType &map)</div><div class="ttdoc">Loads a map from a DTA2D file. </div><div class="ttdef"><b>Definition:</b> DTA2DFile.h:95</div></div>
<div class="ttc" id="KroenikFile_8h_html"><div class="ttname"><a href="KroenikFile_8h.html">KroenikFile.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html_a02fccfed86a20f8bd0f6b98c23fadb2e"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html#a02fccfed86a20f8bd0f6b98c23fadb2e">OpenMS::MSExperiment::getChromatograms</a></div><div class="ttdeci">const std::vector< MSChromatogram< ChromatogramPeakType > > & getChromatograms() const </div><div class="ttdoc">returns the chromatogram list </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:768</div></div>
<div class="ttc" id="classOpenMS_1_1ProgressLogger_html_acc3538c5284777d8702ccaefeb61e74c"><div class="ttname"><a href="classOpenMS_1_1ProgressLogger.html#acc3538c5284777d8702ccaefeb61e74c">OpenMS::ProgressLogger::setLogType</a></div><div class="ttdeci">void setLogType(LogType type) const </div><div class="ttdoc">Sets the progress log that should be used. The default type is NONE! </div></div>
<div class="ttc" id="classOpenMS_1_1ExperimentalSettings_html_a9b357a65e5ec19027b8fa94379439f8c"><div class="ttname"><a href="classOpenMS_1_1ExperimentalSettings.html#a9b357a65e5ec19027b8fa94379439f8c">OpenMS::ExperimentalSettings::getSourceFiles</a></div><div class="ttdeci">const std::vector< SourceFile > & getSourceFiles() const </div><div class="ttdoc">returns a const reference to the source data file </div></div>
<div class="ttc" id="structOpenMS_1_1FileTypes_html_a1d1cfd8ffb84e947f82999c682b666a7af8a53519bd415aacd429c4239bbfd66e"><div class="ttname"><a href="structOpenMS_1_1FileTypes.html#a1d1cfd8ffb84e947f82999c682b666a7af8a53519bd415aacd429c4239bbfd66e">OpenMS::FileTypes::MZXML</a></div><div class="ttdoc">MzXML file (.mzXML) </div><div class="ttdef"><b>Definition:</b> FileTypes.h:65</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 11:19:14 using doxygen 1.8.5</font></TD>
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