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<a href="CachedmzML_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: Hannes Roest $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno"> 32</span> <span class="comment">// $Authors: Hannes Roest $</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_ANALYSIS_OPENSWATH_CACHEDMZML_H</span></div>
<div class="line"><a name="l00036"></a><span class="lineno"> 36</span> <span class="preprocessor"></span><span class="preprocessor">#define OPENMS_ANALYSIS_OPENSWATH_CACHEDMZML_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 <<a class="code" href="ANALYSIS_2OPENSWATH_2OPENSWATHALGO_2DATAACCESS_2ISpectrumAccess_8h.html">OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h</a>></span></div>
<div class="line"><a name="l00039"></a><span class="lineno"> 39</span> </div>
<div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="preprocessor">#include <<a class="code" href="Types_8h.html">OpenMS/CONCEPT/Types.h</a>></span></div>
<div class="line"><a name="l00041"></a><span class="lineno"> 41</span> <span class="preprocessor">#include <<a class="code" href="ProgressLogger_8h.html">OpenMS/CONCEPT/ProgressLogger.h</a>></span></div>
<div class="line"><a name="l00042"></a><span class="lineno"> 42</span> </div>
<div class="line"><a name="l00043"></a><span class="lineno"> 43</span> <span class="preprocessor">#include <<a class="code" href="MSExperiment_8h.html">OpenMS/KERNEL/MSExperiment.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> </div>
<div class="line"><a name="l00046"></a><span class="lineno"> 46</span> <span class="preprocessor">#include <fstream></span></div>
<div class="line"><a name="l00047"></a><span class="lineno"> 47</span> </div>
<div class="line"><a name="l00048"></a><span class="lineno"><a class="line" href="CachedmzML_8h.html#a54061e5993a5517320d425f44408cc86"> 48</a></span> <span class="preprocessor">#define MAGIC_NUMBER 8093</span></div>
<div class="line"><a name="l00049"></a><span class="lineno"> 49</span> <span class="preprocessor"></span></div>
<div class="line"><a name="l00050"></a><span class="lineno"> 50</span> <span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00051"></a><span class="lineno"> 51</span> {</div>
<div class="line"><a name="l00060"></a><span class="lineno"><a class="line" href="classOpenMS_1_1CachedmzML.html"> 60</a></span>  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1CachedmzML.html">CachedmzML</a> :</div>
<div class="line"><a name="l00061"></a><span class="lineno"> 61</span>  <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a></div>
<div class="line"><a name="l00062"></a><span class="lineno"> 62</span>  {</div>
<div class="line"><a name="l00063"></a><span class="lineno"><a class="line" href="classOpenMS_1_1CachedmzML.html#a310dba1a46765ac74b704cfebb30a1ef"> 63</a></span>  <span class="keywordtype">int</span> <a class="code" href="classOpenMS_1_1CachedmzML.html#a310dba1a46765ac74b704cfebb30a1ef">int_field_</a>;</div>
<div class="line"><a name="l00064"></a><span class="lineno"><a class="line" href="classOpenMS_1_1CachedmzML.html#aaaf884a9b63880d037ee5aab0115b567"> 64</a></span>  <span class="keywordtype">double</span> <a class="code" href="classOpenMS_1_1CachedmzML.html#aaaf884a9b63880d037ee5aab0115b567">dbl_field_</a>;</div>
<div class="line"><a name="l00065"></a><span class="lineno"> 65</span> </div>
<div class="line"><a name="l00066"></a><span class="lineno"> 66</span> <span class="keyword">public</span>:</div>
<div class="line"><a name="l00067"></a><span class="lineno"> 67</span> </div>
<div class="line"><a name="l00068"></a><span class="lineno"><a class="line" href="classOpenMS_1_1CachedmzML.html#ab52083d2b64e8db5b7a61c399e288859"> 68</a></span>  <span class="keyword">typedef</span> <a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment<Peak1D></a> <a class="code" href="classOpenMS_1_1CachedmzML.html#ab52083d2b64e8db5b7a61c399e288859">MapType</a>;</div>
<div class="line"><a name="l00069"></a><span class="lineno"><a class="line" href="classOpenMS_1_1CachedmzML.html#a8148ed639ab1958764997633934ddf38"> 69</a></span>  <span class="keyword">typedef</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum<Peak1D></a> <a class="code" href="classOpenMS_1_1CachedmzML.html#a8148ed639ab1958764997633934ddf38">SpectrumType</a>;</div>
<div class="line"><a name="l00070"></a><span class="lineno"><a class="line" href="classOpenMS_1_1CachedmzML.html#acc92c018e6237189da684e845d9b5f9d"> 70</a></span>  <span class="keyword">typedef</span> <a class="code" href="classOpenMS_1_1MSChromatogram.html">MSChromatogram<ChromatogramPeak></a> <a class="code" href="classOpenMS_1_1CachedmzML.html#acc92c018e6237189da684e845d9b5f9d">ChromatogramType</a>;</div>
<div class="line"><a name="l00071"></a><span class="lineno"> 71</span> <span class="preprocessor">#if 1</span></div>
<div class="line"><a name="l00072"></a><span class="lineno"> 72</span> <span class="preprocessor"></span> <span class="comment">// double means twice the file size</span></div>
<div class="line"><a name="l00073"></a><span class="lineno"><a class="line" href="classOpenMS_1_1CachedmzML.html#acbe7ec10442c29895ba7b8881430b10c"> 73</a></span>  <span class="keyword">typedef</span> <span class="keywordtype">double</span> <a class="code" href="classOpenMS_1_1CachedmzML.html#acbe7ec10442c29895ba7b8881430b10c">DatumSingleton</a>;</div>
<div class="line"><a name="l00074"></a><span class="lineno"> 74</span> <span class="preprocessor">#else</span></div>
<div class="line"><a name="l00075"></a><span class="lineno"> 75</span> <span class="preprocessor"></span> <span class="comment">// float means half the file size</span></div>
<div class="line"><a name="l00076"></a><span class="lineno"> 76</span>  <span class="keyword">typedef</span> <span class="keywordtype">float</span> <a class="code" href="classdouble.html">DatumSingleton</a>;</div>
<div class="line"><a name="l00077"></a><span class="lineno"> 77</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00078"></a><span class="lineno"><a class="line" href="classOpenMS_1_1CachedmzML.html#a18bb8f03c608ff0936723df34eef1e2c"> 78</a></span> <span class="preprocessor"></span> <span class="keyword">typedef</span> std::vector<DatumSingleton> <a class="code" href="classOpenMS_1_1CachedmzML.html#a18bb8f03c608ff0936723df34eef1e2c">Datavector</a>;</div>
<div class="line"><a name="l00079"></a><span class="lineno"> 79</span> </div>
<div class="line"><a name="l00083"></a><span class="lineno"> 83</span>  <a class="code" href="classOpenMS_1_1CachedmzML.html">CachedmzML</a>()</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="l00087"></a><span class="lineno"> 87</span> </div>
<div class="line"><a name="l00089"></a><span class="lineno"><a class="line" href="classOpenMS_1_1CachedmzML.html#afe7d98074c75e0f8a4f47299fdebf34e"> 89</a></span>  <a class="code" href="classOpenMS_1_1CachedmzML.html#afe7d98074c75e0f8a4f47299fdebf34e">~CachedmzML</a>()</div>
<div class="line"><a name="l00090"></a><span class="lineno"> 90</span>  {</div>
<div class="line"><a name="l00091"></a><span class="lineno"> 91</span>  }</div>
<div class="line"><a name="l00092"></a><span class="lineno"> 92</span> </div>
<div class="line"><a name="l00094"></a><span class="lineno"><a class="line" href="classOpenMS_1_1CachedmzML.html#a608b23b52372613ab1bcbd1ef741a8e9"> 94</a></span>  <a class="code" href="classOpenMS_1_1CachedmzML.html">CachedmzML</a>& <a class="code" href="classOpenMS_1_1CachedmzML.html#a608b23b52372613ab1bcbd1ef741a8e9">operator=</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1CachedmzML.html">CachedmzML</a>& rhs)</div>
<div class="line"><a name="l00095"></a><span class="lineno"> 95</span>  {</div>
<div class="line"><a name="l00096"></a><span class="lineno"> 96</span>  <span class="keywordflow">if</span> (&rhs == <span class="keyword">this</span>)</div>
<div class="line"><a name="l00097"></a><span class="lineno"> 97</span>  <span class="keywordflow">return</span> *<span class="keyword">this</span>;</div>
<div class="line"><a name="l00098"></a><span class="lineno"> 98</span> </div>
<div class="line"><a name="l00099"></a><span class="lineno"> 99</span>  spectra_index_ = rhs.<a class="code" href="classOpenMS_1_1CachedmzML.html#a094c1fd87db598d60d692ed3f03547ba">spectra_index_</a>;</div>
<div class="line"><a name="l00100"></a><span class="lineno"> 100</span>  chrom_index_ = rhs.<a class="code" href="classOpenMS_1_1CachedmzML.html#a15d13796ad38b3a74526f89cc6b07f01">chrom_index_</a>;</div>
<div class="line"><a name="l00101"></a><span class="lineno"> 101</span> </div>
<div class="line"><a name="l00102"></a><span class="lineno"> 102</span>  <span class="keywordflow">return</span> *<span class="keyword">this</span>;</div>
<div class="line"><a name="l00103"></a><span class="lineno"> 103</span>  }</div>
<div class="line"><a name="l00104"></a><span class="lineno"> 104</span> </div>
<div class="line"><a name="l00106"></a><span class="lineno"> 106</span> </div>
<div class="line"><a name="l00110"></a><span class="lineno"> 110</span>  <span class="keywordtype">void</span> writeMemdump(MapType& exp, <a class="code" href="classOpenMS_1_1String.html">String</a> out)</div>
<div class="line"><a name="l00112"></a><span class="lineno"> 112</span>  {</div>
<div class="line"><a name="l00113"></a><span class="lineno"> 113</span>  std::ofstream ofs(out.c_str(), std::ios::binary);</div>
<div class="line"><a name="l00114"></a><span class="lineno"> 114</span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> exp_size = exp.size();</div>
<div class="line"><a name="l00115"></a><span class="lineno"> 115</span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> chrom_size = exp.getChromatograms().size();</div>
<div class="line"><a name="l00116"></a><span class="lineno"> 116</span>  <span class="keywordtype">int</span> magic_number = <a class="code" href="CachedmzML_8h.html#a54061e5993a5517320d425f44408cc86">MAGIC_NUMBER</a>;</div>
<div class="line"><a name="l00117"></a><span class="lineno"> 117</span>  ofs.write((<span class="keywordtype">char</span>*)&magic_number, <span class="keyword">sizeof</span>(magic_number));</div>
<div class="line"><a name="l00118"></a><span class="lineno"> 118</span>  ofs.write((<span class="keywordtype">char</span>*)&exp_size, <span class="keyword">sizeof</span>(exp_size));</div>
<div class="line"><a name="l00119"></a><span class="lineno"> 119</span>  ofs.write((<span class="keywordtype">char</span>*)&chrom_size, <span class="keyword">sizeof</span>(chrom_size));</div>
<div class="line"><a name="l00120"></a><span class="lineno"> 120</span> </div>
<div class="line"><a name="l00121"></a><span class="lineno"> 121</span>  startProgress(0, exp.size() + exp.getChromatograms().size(), <span class="stringliteral">"storing binary spectra"</span>);</div>
<div class="line"><a name="l00122"></a><span class="lineno"> 122</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i < exp.size(); i++)</div>
<div class="line"><a name="l00123"></a><span class="lineno"> 123</span>  {</div>
<div class="line"><a name="l00124"></a><span class="lineno"> 124</span>  setProgress(i);</div>
<div class="line"><a name="l00125"></a><span class="lineno"> 125</span>  writeSpectrum_(exp[i], ofs);</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> </div>
<div class="line"><a name="l00128"></a><span class="lineno"> 128</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i < exp.getChromatograms().size(); i++)</div>
<div class="line"><a name="l00129"></a><span class="lineno"> 129</span>  {</div>
<div class="line"><a name="l00130"></a><span class="lineno"> 130</span>  setProgress(i);</div>
<div class="line"><a name="l00131"></a><span class="lineno"> 131</span>  writeChromatogram_(exp.getChromatograms()[i], ofs);</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> </div>
<div class="line"><a name="l00134"></a><span class="lineno"> 134</span>  ofs.close();</div>
<div class="line"><a name="l00135"></a><span class="lineno"> 135</span>  endProgress();</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> </div>
<div class="line"><a name="l00139"></a><span class="lineno"><a class="line" href="classOpenMS_1_1CachedmzML.html#a78668c2f83b7e9e4fe595c57ab4c642d"> 139</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1CachedmzML.html#a78668c2f83b7e9e4fe595c57ab4c642d">readMemdump</a>(<a class="code" href="classOpenMS_1_1MSExperiment.html">MapType</a>& exp_reading, <a class="code" href="classOpenMS_1_1String.html">String</a> filename)<span class="keyword"> const</span></div>
<div class="line"><a name="l00140"></a><span class="lineno"> 140</span> <span class="keyword"> </span>{</div>
<div class="line"><a name="l00141"></a><span class="lineno"> 141</span>  std::ifstream ifs(filename.c_str(), std::ios::binary);</div>
<div class="line"><a name="l00142"></a><span class="lineno"> 142</span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> exp_size, chrom_size;</div>
<div class="line"><a name="l00143"></a><span class="lineno"> 143</span>  <a class="code" href="classOpenMS_1_1Peak1D.html">Peak1D</a> current_peak;</div>
<div class="line"><a name="l00144"></a><span class="lineno"> 144</span> </div>
<div class="line"><a name="l00145"></a><span class="lineno"> 145</span>  <span class="keywordtype">int</span> magic_number;</div>
<div class="line"><a name="l00146"></a><span class="lineno"> 146</span>  ifs.read((<span class="keywordtype">char</span>*)&magic_number, <span class="keyword">sizeof</span>(magic_number));</div>
<div class="line"><a name="l00147"></a><span class="lineno"> 147</span>  <span class="keywordflow">if</span> (magic_number != <a class="code" href="CachedmzML_8h.html#a54061e5993a5517320d425f44408cc86">MAGIC_NUMBER</a>)</div>
<div class="line"><a name="l00148"></a><span class="lineno"> 148</span>  {</div>
<div class="line"><a name="l00149"></a><span class="lineno"> 149</span>  <span class="keywordflow">throw</span> <span class="stringliteral">"wrong file, does not start with MAGIC_NUMBER"</span>;</div>
<div class="line"><a name="l00150"></a><span class="lineno"> 150</span>  }</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>  ifs.read((<span class="keywordtype">char</span>*)&exp_size, <span class="keyword">sizeof</span>(exp_size));</div>
<div class="line"><a name="l00153"></a><span class="lineno"> 153</span>  ifs.read((<span class="keywordtype">char</span>*)&chrom_size, <span class="keyword">sizeof</span>(chrom_size));</div>
<div class="line"><a name="l00154"></a><span class="lineno"> 154</span> </div>
<div class="line"><a name="l00155"></a><span class="lineno"> 155</span>  exp_reading.<a class="code" href="classOpenMS_1_1MSExperiment.html#af5e67d26823ec12e91434f4e74faa9d1">reserve</a>(exp_size);</div>
<div class="line"><a name="l00156"></a><span class="lineno"> 156</span>  startProgress(0, exp_size + chrom_size, <span class="stringliteral">"reading binary spectra"</span>);</div>
<div class="line"><a name="l00157"></a><span class="lineno"> 157</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i < exp_size; i++)</div>
<div class="line"><a name="l00158"></a><span class="lineno"> 158</span>  {</div>
<div class="line"><a name="l00159"></a><span class="lineno"> 159</span>  setProgress(i);</div>
<div class="line"><a name="l00160"></a><span class="lineno"> 160</span>  <a class="code" href="classOpenMS_1_1MSSpectrum.html">SpectrumType</a> spectrum;</div>
<div class="line"><a name="l00161"></a><span class="lineno"> 161</span>  readSpectrum_(spectrum, ifs);</div>
<div class="line"><a name="l00162"></a><span class="lineno"> 162</span>  exp_reading.<a class="code" href="classOpenMS_1_1MSExperiment.html#ae9dafbb74a1a4c430ceef03e25ab8e10">addSpectrum</a>(spectrum);</div>
<div class="line"><a name="l00163"></a><span class="lineno"> 163</span>  }</div>
<div class="line"><a name="l00164"></a><span class="lineno"> 164</span>  std::vector<ChromatogramType> chromatograms;</div>
<div class="line"><a name="l00165"></a><span class="lineno"> 165</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i < chrom_size; i++)</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>  setProgress(i);</div>
<div class="line"><a name="l00168"></a><span class="lineno"> 168</span>  <a class="code" href="classOpenMS_1_1MSChromatogram.html">ChromatogramType</a> chromatogram;</div>
<div class="line"><a name="l00169"></a><span class="lineno"> 169</span>  readChromatogram_(chromatogram, ifs);</div>
<div class="line"><a name="l00170"></a><span class="lineno"> 170</span>  chromatograms.push_back(chromatogram);</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>  exp_reading.<a class="code" href="classOpenMS_1_1MSExperiment.html#a4c105ad43f3c61a53997af8ba28720e2">setChromatograms</a>(chromatograms);</div>
<div class="line"><a name="l00173"></a><span class="lineno"> 173</span> </div>
<div class="line"><a name="l00174"></a><span class="lineno"> 174</span>  ifs.close();</div>
<div class="line"><a name="l00175"></a><span class="lineno"> 175</span>  endProgress();</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> </div>
<div class="line"><a name="l00179"></a><span class="lineno"> 179</span> </div>
<div class="line"><a name="l00183"></a><span class="lineno"> 183</span>  <span class="keywordtype">void</span> readSingleSpectrum(<a class="code" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum<Peak1D></a>& spectrum, <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="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a>& idx)<span class="keyword"> const</span></div>
<div class="line"><a name="l00185"></a><span class="lineno"> 185</span> <span class="keyword"> </span>{</div>
<div class="line"><a name="l00186"></a><span class="lineno"> 186</span>  <span class="comment">// open stream, read</span></div>
<div class="line"><a name="l00187"></a><span class="lineno"> 187</span>  std::ifstream ifs(filename.c_str(), std::ios::binary);</div>
<div class="line"><a name="l00188"></a><span class="lineno"> 188</span>  readSingleSpectrum(spectrum, ifs, idx);</div>
<div class="line"><a name="l00189"></a><span class="lineno"> 189</span>  }</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>  <span class="comment">// Read a single spectrum from the given filestream</span></div>
<div class="line"><a name="l00192"></a><span class="lineno"><a class="line" href="classOpenMS_1_1CachedmzML.html#ae1739688d14fd48cfe0237b6033a56fc"> 192</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1CachedmzML.html#ae1739688d14fd48cfe0237b6033a56fc">readSingleSpectrum</a>(<a class="code" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum<Peak1D></a>& spectrum, std::ifstream& ifs, <span class="keyword">const</span> <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a>& idx)<span class="keyword"> const</span></div>
<div class="line"><a name="l00193"></a><span class="lineno"> 193</span> <span class="keyword"> </span>{</div>
<div class="line"><a name="l00194"></a><span class="lineno"> 194</span>  <span class="comment">// go to the specified index</span></div>
<div class="line"><a name="l00195"></a><span class="lineno"> 195</span>  ifs.seekg(idx);</div>
<div class="line"><a name="l00196"></a><span class="lineno"> 196</span>  readSpectrum_(spectrum, ifs);</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> </div>
<div class="line"><a name="l00200"></a><span class="lineno"> 200</span> </div>
<div class="line"><a name="l00204"></a><span class="lineno"><a class="line" href="classOpenMS_1_1CachedmzML.html#adde8fb22b8fbfc4d985d8a8467ad91f5"> 204</a></span>  <span class="keyword">const</span> std::vector<Size>& <a class="code" href="classOpenMS_1_1CachedmzML.html#adde8fb22b8fbfc4d985d8a8467ad91f5">getSpectraIndex</a>()<span class="keyword"> const</span></div>
<div class="line"><a name="l00205"></a><span class="lineno"> 205</span> <span class="keyword"> </span>{</div>
<div class="line"><a name="l00206"></a><span class="lineno"> 206</span>  <span class="keywordflow">return</span> spectra_index_;</div>
<div class="line"><a name="l00207"></a><span class="lineno"> 207</span>  }</div>
<div class="line"><a name="l00208"></a><span class="lineno"> 208</span> </div>
<div class="line"><a name="l00209"></a><span class="lineno"><a class="line" href="classOpenMS_1_1CachedmzML.html#a4a462892f19dc42bfeb2f1b67098eba9"> 209</a></span>  <span class="keyword">const</span> std::vector<Size>& <a class="code" href="classOpenMS_1_1CachedmzML.html#a4a462892f19dc42bfeb2f1b67098eba9">getChromatogramIndex</a>()<span class="keyword"> const</span></div>
<div class="line"><a name="l00210"></a><span class="lineno"> 210</span> <span class="keyword"> </span>{</div>
<div class="line"><a name="l00211"></a><span class="lineno"> 211</span>  <span class="keywordflow">return</span> chrom_index_;</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> </div>
<div class="line"><a name="l00215"></a><span class="lineno"> 215</span> </div>
<div class="line"><a name="l00217"></a><span class="lineno"><a class="line" href="classOpenMS_1_1CachedmzML.html#ac37f5b61a6e64df22f26f98cd9f4f6d5"> 217</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1CachedmzML.html#ac37f5b61a6e64df22f26f98cd9f4f6d5">createMemdumpIndex</a>(<a class="code" href="classOpenMS_1_1String.html">String</a> filename)</div>
<div class="line"><a name="l00218"></a><span class="lineno"> 218</span>  {</div>
<div class="line"><a name="l00219"></a><span class="lineno"> 219</span>  std::ifstream ifs(filename.c_str(), std::ios::binary);</div>
<div class="line"><a name="l00220"></a><span class="lineno"> 220</span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> exp_size, chrom_size;</div>
<div class="line"><a name="l00221"></a><span class="lineno"> 221</span>  <a class="code" href="classOpenMS_1_1Peak1D.html">Peak1D</a> current_peak;</div>
<div class="line"><a name="l00222"></a><span class="lineno"> 222</span> </div>
<div class="line"><a name="l00223"></a><span class="lineno"> 223</span>  spectra_index_.clear();</div>
<div class="line"><a name="l00224"></a><span class="lineno"> 224</span>  chrom_index_.clear();</div>
<div class="line"><a name="l00225"></a><span class="lineno"> 225</span>  <span class="keywordtype">int</span> magic_number;</div>
<div class="line"><a name="l00226"></a><span class="lineno"> 226</span>  <span class="keywordtype">int</span> extra_offset = <span class="keyword">sizeof</span>(dbl_field_) + <span class="keyword">sizeof</span>(int_field_);</div>
<div class="line"><a name="l00227"></a><span class="lineno"> 227</span>  <span class="keywordtype">int</span> chrom_offset = 0;</div>
<div class="line"><a name="l00228"></a><span class="lineno"> 228</span> </div>
<div class="line"><a name="l00229"></a><span class="lineno"> 229</span>  ifs.read((<span class="keywordtype">char</span>*)&magic_number, <span class="keyword">sizeof</span>(magic_number));</div>
<div class="line"><a name="l00230"></a><span class="lineno"> 230</span>  <span class="keywordflow">if</span> (magic_number != <a class="code" href="CachedmzML_8h.html#a54061e5993a5517320d425f44408cc86">MAGIC_NUMBER</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>  <span class="keywordflow">throw</span> <span class="stringliteral">"wrong file, does not start with MAGIC_NUMBER"</span>;</div>
<div class="line"><a name="l00233"></a><span class="lineno"> 233</span>  }</div>
<div class="line"><a name="l00234"></a><span class="lineno"> 234</span> </div>
<div class="line"><a name="l00235"></a><span class="lineno"> 235</span>  <span class="comment">// For spectra and chromatograms go through file, read the size of the</span></div>
<div class="line"><a name="l00236"></a><span class="lineno"> 236</span>  <span class="comment">// spectrum/chromatogram and record the starting index of the element, then</span></div>
<div class="line"><a name="l00237"></a><span class="lineno"> 237</span>  <span class="comment">// skip ahead to the next spectrum/chromatogram.</span></div>
<div class="line"><a name="l00238"></a><span class="lineno"> 238</span>  ifs.read((<span class="keywordtype">char</span>*)&exp_size, <span class="keyword">sizeof</span>(exp_size));</div>
<div class="line"><a name="l00239"></a><span class="lineno"> 239</span>  ifs.read((<span class="keywordtype">char</span>*)&chrom_size, <span class="keyword">sizeof</span>(chrom_size));</div>
<div class="line"><a name="l00240"></a><span class="lineno"> 240</span>  startProgress(0, exp_size + chrom_size, <span class="stringliteral">"Creating index for binary spectra"</span>);</div>
<div class="line"><a name="l00241"></a><span class="lineno"> 241</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i < exp_size; i++)</div>
<div class="line"><a name="l00242"></a><span class="lineno"> 242</span>  {</div>
<div class="line"><a name="l00243"></a><span class="lineno"> 243</span>  setProgress(i);</div>
<div class="line"><a name="l00244"></a><span class="lineno"> 244</span> </div>
<div class="line"><a name="l00245"></a><span class="lineno"> 245</span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> spec_size;</div>
<div class="line"><a name="l00246"></a><span class="lineno"> 246</span>  spectra_index_.push_back(ifs.tellg());</div>
<div class="line"><a name="l00247"></a><span class="lineno"> 247</span>  ifs.read((<span class="keywordtype">char</span>*)&spec_size, <span class="keyword">sizeof</span>(spec_size));</div>
<div class="line"><a name="l00248"></a><span class="lineno"> 248</span>  ifs.seekg((<span class="keywordtype">int</span>)ifs.tellg() + extra_offset + (<span class="keyword">sizeof</span>(<a class="code" href="classdouble.html">DatumSingleton</a>)) * 2 * (spec_size));</div>
<div class="line"><a name="l00249"></a><span class="lineno"> 249</span> </div>
<div class="line"><a name="l00250"></a><span class="lineno"> 250</span>  }</div>
<div class="line"><a name="l00251"></a><span class="lineno"> 251</span> </div>
<div class="line"><a name="l00252"></a><span class="lineno"> 252</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i < chrom_size; i++)</div>
<div class="line"><a name="l00253"></a><span class="lineno"> 253</span>  {</div>
<div class="line"><a name="l00254"></a><span class="lineno"> 254</span>  setProgress(i);</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>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> chrom_size;</div>
<div class="line"><a name="l00257"></a><span class="lineno"> 257</span>  chrom_index_.push_back(ifs.tellg());</div>
<div class="line"><a name="l00258"></a><span class="lineno"> 258</span>  ifs.read((<span class="keywordtype">char</span>*)&chrom_size, <span class="keyword">sizeof</span>(chrom_size));</div>
<div class="line"><a name="l00259"></a><span class="lineno"> 259</span>  ifs.seekg((<span class="keywordtype">int</span>)ifs.tellg() + chrom_offset + (<span class="keyword">sizeof</span>(<a class="code" href="classdouble.html">DatumSingleton</a>)) * 2 * (chrom_size));</div>
<div class="line"><a name="l00260"></a><span class="lineno"> 260</span> </div>
<div class="line"><a name="l00261"></a><span class="lineno"> 261</span>  }</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>  ifs.close();</div>
<div class="line"><a name="l00264"></a><span class="lineno"> 264</span>  endProgress();</div>
<div class="line"><a name="l00265"></a><span class="lineno"> 265</span>  }</div>
<div class="line"><a name="l00266"></a><span class="lineno"> 266</span> </div>
<div class="line"><a name="l00268"></a><span class="lineno"><a class="line" href="classOpenMS_1_1CachedmzML.html#ad117b85f93b2c7c04b5031c4d6f70a9f"> 268</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1CachedmzML.html#ad117b85f93b2c7c04b5031c4d6f70a9f">writeMetadata</a>(<a class="code" href="classOpenMS_1_1MSExperiment.html">MapType</a> exp, <a class="code" href="classOpenMS_1_1String.html">String</a> out_meta)</div>
<div class="line"><a name="l00269"></a><span class="lineno"> 269</span>  {</div>
<div class="line"><a name="l00270"></a><span class="lineno"> 270</span>  <span class="comment">// delete the actual data for all spectra and chromatograms, leave only metadata</span></div>
<div class="line"><a name="l00271"></a><span class="lineno"> 271</span>  std::vector<MSChromatogram<ChromatogramPeak> > chromatograms = exp.<a class="code" href="classOpenMS_1_1MSExperiment.html#a02fccfed86a20f8bd0f6b98c23fadb2e">getChromatograms</a>(); <span class="comment">// copy</span></div>
<div class="line"><a name="l00272"></a><span class="lineno"> 272</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i < exp.<a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>(); i++)</div>
<div class="line"><a name="l00273"></a><span class="lineno"> 273</span>  {</div>
<div class="line"><a name="l00274"></a><span class="lineno"> 274</span>  exp[i].<a class="code" href="classOpenMS_1_1MSExperiment.html#af072fc84225ae927f7527f208ea86cbd">clear</a>(<span class="keyword">false</span>);</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">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i < exp.<a class="code" href="classOpenMS_1_1MSExperiment.html#a02fccfed86a20f8bd0f6b98c23fadb2e">getChromatograms</a>().size(); i++)</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>  <span class="comment">// delete the actual data, leave only metadata</span></div>
<div class="line"><a name="l00279"></a><span class="lineno"> 279</span>  <span class="comment">//exp.getChromatograms()[i].clear(false);</span></div>
<div class="line"><a name="l00280"></a><span class="lineno"> 280</span>  chromatograms[i].clear(<span class="keyword">false</span>);</div>
<div class="line"><a name="l00281"></a><span class="lineno"> 281</span>  }</div>
<div class="line"><a name="l00282"></a><span class="lineno"> 282</span>  exp.<a class="code" href="classOpenMS_1_1MSExperiment.html#a4c105ad43f3c61a53997af8ba28720e2">setChromatograms</a>(chromatograms);</div>
<div class="line"><a name="l00283"></a><span class="lineno"> 283</span> </div>
<div class="line"><a name="l00284"></a><span class="lineno"> 284</span>  <span class="comment">// store the meta data that is left in out_meta file</span></div>
<div class="line"><a name="l00285"></a><span class="lineno"> 285</span>  <a class="code" href="classOpenMS_1_1MzMLFile.html">MzMLFile</a> f;</div>
<div class="line"><a name="l00286"></a><span class="lineno"> 286</span>  f.<a class="code" href="classOpenMS_1_1MzMLFile.html#adb795d215478320be7c6130ff7ddf853">store</a>(out_meta, exp);</div>
<div class="line"><a name="l00287"></a><span class="lineno"> 287</span>  }</div>
<div class="line"><a name="l00288"></a><span class="lineno"> 288</span> </div>
<div class="line"><a name="l00290"></a><span class="lineno"><a class="line" href="classOpenMS_1_1CachedmzML.html#afc7807c8e8c717754f5355d4a85e8ea2"> 290</a></span>  <span class="keyword">static</span> <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1CachedmzML.html#afc7807c8e8c717754f5355d4a85e8ea2">readSpectrumFast</a>(<a class="code" href="namespaceOpenSwath.html#a8aaa5999a567d0b9a393ea480244162b">OpenSwath::BinaryDataArrayPtr</a> data1,</div>
<div class="line"><a name="l00291"></a><span class="lineno"> 291</span>  <a class="code" href="namespaceOpenSwath.html#a8aaa5999a567d0b9a393ea480244162b">OpenSwath::BinaryDataArrayPtr</a> data2, std::ifstream& ifs, <span class="keywordtype">int</span> ms_level,</div>
<div class="line"><a name="l00292"></a><span class="lineno"> 292</span>  <span class="keywordtype">double</span> rt)</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>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> spec_size = -1;</div>
<div class="line"><a name="l00295"></a><span class="lineno"> 295</span>  ifs.read((<span class="keywordtype">char</span>*) &spec_size, <span class="keyword">sizeof</span>(spec_size));</div>
<div class="line"><a name="l00296"></a><span class="lineno"> 296</span>  ifs.read((<span class="keywordtype">char</span>*) &ms_level, <span class="keyword">sizeof</span>(ms_level));</div>
<div class="line"><a name="l00297"></a><span class="lineno"> 297</span>  ifs.read((<span class="keywordtype">char</span>*) &rt, <span class="keyword">sizeof</span>(rt));</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>  data1->data.resize(spec_size);</div>
<div class="line"><a name="l00300"></a><span class="lineno"> 300</span>  data2->data.resize(spec_size);</div>
<div class="line"><a name="l00301"></a><span class="lineno"> 301</span>  ifs.read((<span class="keywordtype">char</span>*) &(data1->data)[0], spec_size * <span class="keyword">sizeof</span>(<span class="keywordtype">double</span>));</div>
<div class="line"><a name="l00302"></a><span class="lineno"> 302</span>  ifs.read((<span class="keywordtype">char</span>*) &(data2->data)[0], spec_size * <span class="keyword">sizeof</span>(<span class="keywordtype">double</span>));</div>
<div class="line"><a name="l00303"></a><span class="lineno"> 303</span>  }</div>
<div class="line"><a name="l00304"></a><span class="lineno"> 304</span> </div>
<div class="line"><a name="l00306"></a><span class="lineno"><a class="line" href="classOpenMS_1_1CachedmzML.html#a5fe3a9e1e476192f7f0e9818cbce3ceb"> 306</a></span>  <span class="keyword">static</span> <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1CachedmzML.html#a5fe3a9e1e476192f7f0e9818cbce3ceb">readChromatogramFast</a>(<a class="code" href="namespaceOpenSwath.html#a8aaa5999a567d0b9a393ea480244162b">OpenSwath::BinaryDataArrayPtr</a> data1,</div>
<div class="line"><a name="l00307"></a><span class="lineno"> 307</span>  <a class="code" href="namespaceOpenSwath.html#a8aaa5999a567d0b9a393ea480244162b">OpenSwath::BinaryDataArrayPtr</a> data2, std::ifstream& ifs)</div>
<div class="line"><a name="l00308"></a><span class="lineno"> 308</span>  {</div>
<div class="line"><a name="l00309"></a><span class="lineno"> 309</span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> spec_size = -1;</div>
<div class="line"><a name="l00310"></a><span class="lineno"> 310</span>  ifs.read((<span class="keywordtype">char</span>*) &spec_size, <span class="keyword">sizeof</span>(spec_size));</div>
<div class="line"><a name="l00311"></a><span class="lineno"> 311</span>  data1->data.resize(spec_size);</div>
<div class="line"><a name="l00312"></a><span class="lineno"> 312</span> </div>
<div class="line"><a name="l00313"></a><span class="lineno"> 313</span>  data2->data.resize(spec_size);</div>
<div class="line"><a name="l00314"></a><span class="lineno"> 314</span>  ifs.read((<span class="keywordtype">char</span>*) &(data1->data)[0], spec_size * <span class="keyword">sizeof</span>(<span class="keywordtype">double</span>));</div>
<div class="line"><a name="l00315"></a><span class="lineno"> 315</span>  ifs.read((<span class="keywordtype">char</span>*) &(data2->data)[0], spec_size * <span class="keyword">sizeof</span>(<span class="keywordtype">double</span>));</div>
<div class="line"><a name="l00316"></a><span class="lineno"> 316</span>  }</div>
<div class="line"><a name="l00317"></a><span class="lineno"> 317</span> </div>
<div class="line"><a name="l00318"></a><span class="lineno"> 318</span> <span class="keyword">protected</span>:</div>
<div class="line"><a name="l00319"></a><span class="lineno"> 319</span> </div>
<div class="line"><a name="l00320"></a><span class="lineno"> 320</span>  <span class="comment">// read a single spectrum directly into a datavector (assuming file is already at the correct position)</span></div>
<div class="line"><a name="l00321"></a><span class="lineno"><a class="line" href="classOpenMS_1_1CachedmzML.html#aeef724ccc70a46b7a027d2f0db112ea0"> 321</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1CachedmzML.html#aeef724ccc70a46b7a027d2f0db112ea0">readSpectrum_</a>(<a class="code" href="classOpenMS_1_1CachedmzML.html#a18bb8f03c608ff0936723df34eef1e2c">Datavector</a>& data1, <a class="code" href="classOpenMS_1_1CachedmzML.html#a18bb8f03c608ff0936723df34eef1e2c">Datavector</a>& data2, std::ifstream& ifs, <span class="keywordtype">int</span>& ms_level, <span class="keywordtype">double</span>& rt)<span class="keyword"> const</span></div>
<div class="line"><a name="l00322"></a><span class="lineno"> 322</span> <span class="keyword"> </span>{</div>
<div class="line"><a name="l00323"></a><span class="lineno"> 323</span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> spec_size = -1;</div>
<div class="line"><a name="l00324"></a><span class="lineno"> 324</span>  ifs.read((<span class="keywordtype">char</span>*)&spec_size, <span class="keyword">sizeof</span>(spec_size));</div>
<div class="line"><a name="l00325"></a><span class="lineno"> 325</span>  ifs.read((<span class="keywordtype">char</span>*)&ms_level, <span class="keyword">sizeof</span>(ms_level));</div>
<div class="line"><a name="l00326"></a><span class="lineno"> 326</span>  ifs.read((<span class="keywordtype">char</span>*)&rt, <span class="keyword">sizeof</span>(rt));</div>
<div class="line"><a name="l00327"></a><span class="lineno"> 327</span> </div>
<div class="line"><a name="l00328"></a><span class="lineno"> 328</span>  data1.resize(spec_size);</div>
<div class="line"><a name="l00329"></a><span class="lineno"> 329</span>  data2.resize(spec_size);</div>
<div class="line"><a name="l00330"></a><span class="lineno"> 330</span>  ifs.read((<span class="keywordtype">char</span>*)&data1[0], spec_size * <span class="keyword">sizeof</span>(<a class="code" href="classdouble.html">DatumSingleton</a>));</div>
<div class="line"><a name="l00331"></a><span class="lineno"> 331</span>  ifs.read((<span class="keywordtype">char</span>*)&data2[0], spec_size * <span class="keyword">sizeof</span>(<a class="code" href="classdouble.html">DatumSingleton</a>));</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> </div>
<div class="line"><a name="l00334"></a><span class="lineno"> 334</span>  <span class="comment">// read a single chromatogram directly into a datavector (assuming file is already at the correct position)</span></div>
<div class="line"><a name="l00335"></a><span class="lineno"><a class="line" href="classOpenMS_1_1CachedmzML.html#ad4ab33d391cc72c4b5e1720588a41958"> 335</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1CachedmzML.html#ad4ab33d391cc72c4b5e1720588a41958">readChromatogram_</a>(<a class="code" href="classOpenMS_1_1CachedmzML.html#a18bb8f03c608ff0936723df34eef1e2c">Datavector</a>& data1, <a class="code" href="classOpenMS_1_1CachedmzML.html#a18bb8f03c608ff0936723df34eef1e2c">Datavector</a>& data2, std::ifstream& ifs)<span class="keyword"> const</span></div>
<div class="line"><a name="l00336"></a><span class="lineno"> 336</span> <span class="keyword"> </span>{</div>
<div class="line"><a name="l00337"></a><span class="lineno"> 337</span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> spec_size = -1;</div>
<div class="line"><a name="l00338"></a><span class="lineno"> 338</span>  ifs.read((<span class="keywordtype">char</span>*)&spec_size, <span class="keyword">sizeof</span>(spec_size));</div>
<div class="line"><a name="l00339"></a><span class="lineno"> 339</span>  data1.resize(spec_size);</div>
<div class="line"><a name="l00340"></a><span class="lineno"> 340</span>  data2.resize(spec_size);</div>
<div class="line"><a name="l00341"></a><span class="lineno"> 341</span>  ifs.read((<span class="keywordtype">char</span>*)&data1[0], spec_size * <span class="keyword">sizeof</span>(<a class="code" href="classdouble.html">DatumSingleton</a>));</div>
<div class="line"><a name="l00342"></a><span class="lineno"> 342</span>  ifs.read((<span class="keywordtype">char</span>*)&data2[0], spec_size * <span class="keyword">sizeof</span>(<a class="code" href="classdouble.html">DatumSingleton</a>));</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">// read a single spectrum directly into an OpenMS MSSpectrum (assuming file is already at the correct position)</span></div>
<div class="line"><a name="l00346"></a><span class="lineno"><a class="line" href="classOpenMS_1_1CachedmzML.html#a357a85b39a2e70c765e95f12cf46579c"> 346</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1CachedmzML.html#a357a85b39a2e70c765e95f12cf46579c">readSpectrum_</a>(<a class="code" href="classOpenMS_1_1MSSpectrum.html">SpectrumType</a>& spectrum, std::ifstream& ifs)<span class="keyword"> const</span></div>
<div class="line"><a name="l00347"></a><span class="lineno"> 347</span> <span class="keyword"> </span>{</div>
<div class="line"><a name="l00348"></a><span class="lineno"> 348</span>  <a class="code" href="classOpenMS_1_1CachedmzML.html#a18bb8f03c608ff0936723df34eef1e2c">Datavector</a> mz_data;</div>
<div class="line"><a name="l00349"></a><span class="lineno"> 349</span>  <a class="code" href="classOpenMS_1_1CachedmzML.html#a18bb8f03c608ff0936723df34eef1e2c">Datavector</a> int_data;</div>
<div class="line"><a name="l00350"></a><span class="lineno"> 350</span> </div>
<div class="line"><a name="l00351"></a><span class="lineno"> 351</span>  <span class="keywordtype">int</span> ms_level;</div>
<div class="line"><a name="l00352"></a><span class="lineno"> 352</span>  <span class="keywordtype">double</span> rt;</div>
<div class="line"><a name="l00353"></a><span class="lineno"> 353</span>  readSpectrum_(mz_data, int_data, ifs, ms_level, rt);</div>
<div class="line"><a name="l00354"></a><span class="lineno"> 354</span>  spectrum.reserve(mz_data.size());</div>
<div class="line"><a name="l00355"></a><span class="lineno"> 355</span>  spectrum.<a class="code" href="classOpenMS_1_1MSSpectrum.html#a24f081fe74bbbf773533ad19e96d8358">setMSLevel</a>(ms_level);</div>
<div class="line"><a name="l00356"></a><span class="lineno"> 356</span>  spectrum.<a class="code" href="classOpenMS_1_1MSSpectrum.html#aac8c50f318154e9e5b7b01aee806e17f">setRT</a>(rt);</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">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> j = 0; j < mz_data.size(); j++)</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_1Peak1D.html">Peak1D</a> p;</div>
<div class="line"><a name="l00361"></a><span class="lineno"> 361</span>  p.<a class="code" href="classOpenMS_1_1Peak1D.html#ab9c4ce5d172a75d6de2c6f5f1847c9ab">setMZ</a>(mz_data[j]);</div>
<div class="line"><a name="l00362"></a><span class="lineno"> 362</span>  p.<a class="code" href="classOpenMS_1_1Peak1D.html#ab875c2479c6cd2a0189e4684bfa4f97d">setIntensity</a>(int_data[j]);</div>
<div class="line"><a name="l00363"></a><span class="lineno"> 363</span>  spectrum.push_back(p);</div>
<div class="line"><a name="l00364"></a><span class="lineno"> 364</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> </div>
<div class="line"><a name="l00368"></a><span class="lineno"> 368</span>  <span class="comment">// read a single chromatogram directly into an OpenMS MSChromatograms (assuming file is already at the correct position)</span></div>
<div class="line"><a name="l00369"></a><span class="lineno"><a class="line" href="classOpenMS_1_1CachedmzML.html#a3dc2908daf773558c67dca821c1d0ae7"> 369</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1CachedmzML.html#a3dc2908daf773558c67dca821c1d0ae7">readChromatogram_</a>(<a class="code" href="classOpenMS_1_1MSChromatogram.html">ChromatogramType</a>& chromatogram, std::ifstream& ifs)<span class="keyword"> const</span></div>
<div class="line"><a name="l00370"></a><span class="lineno"> 370</span> <span class="keyword"> </span>{</div>
<div class="line"><a name="l00371"></a><span class="lineno"> 371</span>  <a class="code" href="classOpenMS_1_1CachedmzML.html#a18bb8f03c608ff0936723df34eef1e2c">Datavector</a> rt_data;</div>
<div class="line"><a name="l00372"></a><span class="lineno"> 372</span>  <a class="code" href="classOpenMS_1_1CachedmzML.html#a18bb8f03c608ff0936723df34eef1e2c">Datavector</a> int_data;</div>
<div class="line"><a name="l00373"></a><span class="lineno"> 373</span>  readChromatogram_(rt_data, int_data, ifs);</div>
<div class="line"><a name="l00374"></a><span class="lineno"> 374</span>  chromatogram.reserve(rt_data.size());</div>
<div class="line"><a name="l00375"></a><span class="lineno"> 375</span> </div>
<div class="line"><a name="l00376"></a><span class="lineno"> 376</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> j = 0; j < rt_data.size(); j++)</div>
<div class="line"><a name="l00377"></a><span class="lineno"> 377</span>  {</div>
<div class="line"><a name="l00378"></a><span class="lineno"> 378</span>  <a class="code" href="classOpenMS_1_1ChromatogramPeak.html">ChromatogramPeak</a> p;</div>
<div class="line"><a name="l00379"></a><span class="lineno"> 379</span>  p.<a class="code" href="classOpenMS_1_1ChromatogramPeak.html#a98fe0c3fba1788864d35d8ef6159459f">setRT</a>(rt_data[j]);</div>
<div class="line"><a name="l00380"></a><span class="lineno"> 380</span>  p.<a class="code" href="classOpenMS_1_1ChromatogramPeak.html#ab875c2479c6cd2a0189e4684bfa4f97d">setIntensity</a>(int_data[j]);</div>
<div class="line"><a name="l00381"></a><span class="lineno"> 381</span>  chromatogram.push_back(p);</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> </div>
<div class="line"><a name="l00384"></a><span class="lineno"> 384</span>  }</div>
<div class="line"><a name="l00385"></a><span class="lineno"> 385</span> </div>
<div class="line"><a name="l00386"></a><span class="lineno"> 386</span>  <span class="comment">// write a single spectrum to filestream</span></div>
<div class="line"><a name="l00387"></a><span class="lineno"><a class="line" href="classOpenMS_1_1CachedmzML.html#a898c0cb00444946a2de2e4c77b0c3d17"> 387</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1CachedmzML.html#a898c0cb00444946a2de2e4c77b0c3d17">writeSpectrum_</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html">SpectrumType</a>& spectrum, std::ofstream& ofs)</div>
<div class="line"><a name="l00388"></a><span class="lineno"> 388</span>  {</div>
<div class="line"><a name="l00389"></a><span class="lineno"> 389</span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> exp_size = spectrum.size();</div>
<div class="line"><a name="l00390"></a><span class="lineno"> 390</span>  ofs.write((<span class="keywordtype">char</span>*)&exp_size, <span class="keyword">sizeof</span>(exp_size));</div>
<div class="line"><a name="l00391"></a><span class="lineno"> 391</span>  int_field_ = spectrum.<a class="code" href="classOpenMS_1_1MSSpectrum.html#a1726d12d7597baa9fca0c1da0492f3da">getMSLevel</a>();</div>
<div class="line"><a name="l00392"></a><span class="lineno"> 392</span>  ofs.write((<span class="keywordtype">char</span>*)&int_field_, <span class="keyword">sizeof</span>(int_field_));</div>
<div class="line"><a name="l00393"></a><span class="lineno"> 393</span>  dbl_field_ = spectrum.<a class="code" href="classOpenMS_1_1MSSpectrum.html#a3da529bd3240fa0d7148484bbef0b9d7">getRT</a>();</div>
<div class="line"><a name="l00394"></a><span class="lineno"> 394</span>  ofs.write((<span class="keywordtype">char</span>*)&dbl_field_, <span class="keyword">sizeof</span>(dbl_field_));</div>
<div class="line"><a name="l00395"></a><span class="lineno"> 395</span> </div>
<div class="line"><a name="l00396"></a><span class="lineno"> 396</span> <span class="preprocessor">#if 0</span></div>
<div class="line"><a name="l00397"></a><span class="lineno"> 397</span> <span class="preprocessor"></span> ofs.write((<span class="keywordtype">char</span>*)&exp[i].front(), exp[i].size() * <span class="keyword">sizeof</span>(exp[i].front()));</div>
<div class="line"><a name="l00398"></a><span class="lineno"> 398</span>  std::cout << <span class="stringliteral">" storing spectrum "</span> << i << <span class="stringliteral">" with size "</span> << exp[i].size() << std::endl;</div>
<div class="line"><a name="l00399"></a><span class="lineno"> 399</span> <span class="preprocessor">#else</span></div>
<div class="line"><a name="l00400"></a><span class="lineno"> 400</span> <span class="preprocessor"></span> <a class="code" href="classOpenMS_1_1CachedmzML.html#a18bb8f03c608ff0936723df34eef1e2c">Datavector</a> mz_data;</div>
<div class="line"><a name="l00401"></a><span class="lineno"> 401</span>  <a class="code" href="classOpenMS_1_1CachedmzML.html#a18bb8f03c608ff0936723df34eef1e2c">Datavector</a> int_data;</div>
<div class="line"><a name="l00402"></a><span class="lineno"> 402</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> j = 0; j < spectrum.size(); j++)</div>
<div class="line"><a name="l00403"></a><span class="lineno"> 403</span>  {</div>
<div class="line"><a name="l00404"></a><span class="lineno"> 404</span>  mz_data.push_back(spectrum[j].getMZ());</div>
<div class="line"><a name="l00405"></a><span class="lineno"> 405</span>  int_data.push_back(spectrum[j].getIntensity());</div>
<div class="line"><a name="l00406"></a><span class="lineno"> 406</span>  }</div>
<div class="line"><a name="l00407"></a><span class="lineno"> 407</span>  ofs.write((<span class="keywordtype">char</span>*)&mz_data.front(), mz_data.size() * <span class="keyword">sizeof</span>(mz_data.front()));</div>
<div class="line"><a name="l00408"></a><span class="lineno"> 408</span>  ofs.write((<span class="keywordtype">char</span>*)&int_data.front(), int_data.size() * <span class="keyword">sizeof</span>(int_data.front()));</div>
<div class="line"><a name="l00409"></a><span class="lineno"> 409</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00410"></a><span class="lineno"> 410</span> <span class="preprocessor"></span> <span class="comment">//std::cout << exp[i] << std::endl;</span></div>
<div class="line"><a name="l00411"></a><span class="lineno"> 411</span>  }</div>
<div class="line"><a name="l00412"></a><span class="lineno"> 412</span> </div>
<div class="line"><a name="l00413"></a><span class="lineno"> 413</span>  <span class="comment">// write a single chromatogram to filestream</span></div>
<div class="line"><a name="l00414"></a><span class="lineno"><a class="line" href="classOpenMS_1_1CachedmzML.html#af84b721d86630a1d8f05c4389070831b"> 414</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1CachedmzML.html#af84b721d86630a1d8f05c4389070831b">writeChromatogram_</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSChromatogram.html">ChromatogramType</a>& chromatogram, std::ofstream& ofs)</div>
<div class="line"><a name="l00415"></a><span class="lineno"> 415</span>  {</div>
<div class="line"><a name="l00416"></a><span class="lineno"> 416</span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> exp_size = chromatogram.size();</div>
<div class="line"><a name="l00417"></a><span class="lineno"> 417</span>  ofs.write((<span class="keywordtype">char</span>*)&exp_size, <span class="keyword">sizeof</span>(exp_size));</div>
<div class="line"><a name="l00418"></a><span class="lineno"> 418</span>  <a class="code" href="classOpenMS_1_1CachedmzML.html#a18bb8f03c608ff0936723df34eef1e2c">Datavector</a> rt_data;</div>
<div class="line"><a name="l00419"></a><span class="lineno"> 419</span>  <a class="code" href="classOpenMS_1_1CachedmzML.html#a18bb8f03c608ff0936723df34eef1e2c">Datavector</a> int_data;</div>
<div class="line"><a name="l00420"></a><span class="lineno"> 420</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> j = 0; j < chromatogram.size(); j++)</div>
<div class="line"><a name="l00421"></a><span class="lineno"> 421</span>  {</div>
<div class="line"><a name="l00422"></a><span class="lineno"> 422</span>  rt_data.push_back(chromatogram[j].getRT());</div>
<div class="line"><a name="l00423"></a><span class="lineno"> 423</span>  int_data.push_back(chromatogram[j].getIntensity());</div>
<div class="line"><a name="l00424"></a><span class="lineno"> 424</span>  }</div>
<div class="line"><a name="l00425"></a><span class="lineno"> 425</span>  ofs.write((<span class="keywordtype">char</span>*)&rt_data.front(), rt_data.size() * <span class="keyword">sizeof</span>(rt_data.front()));</div>
<div class="line"><a name="l00426"></a><span class="lineno"> 426</span>  ofs.write((<span class="keywordtype">char</span>*)&int_data.front(), int_data.size() * <span class="keyword">sizeof</span>(int_data.front()));</div>
<div class="line"><a name="l00427"></a><span class="lineno"> 427</span>  }</div>
<div class="line"><a name="l00428"></a><span class="lineno"> 428</span> </div>
<div class="line"><a name="l00429"></a><span class="lineno"><a class="line" href="classOpenMS_1_1CachedmzML.html#a094c1fd87db598d60d692ed3f03547ba"> 429</a></span>  std::vector<Size> <a class="code" href="classOpenMS_1_1CachedmzML.html#a094c1fd87db598d60d692ed3f03547ba">spectra_index_</a>;</div>
<div class="line"><a name="l00430"></a><span class="lineno"><a class="line" href="classOpenMS_1_1CachedmzML.html#a15d13796ad38b3a74526f89cc6b07f01"> 430</a></span>  std::vector<Size> <a class="code" href="classOpenMS_1_1CachedmzML.html#a15d13796ad38b3a74526f89cc6b07f01">chrom_index_</a>;</div>
<div class="line"><a name="l00431"></a><span class="lineno"> 431</span> </div>
<div class="line"><a name="l00432"></a><span class="lineno"> 432</span>  };</div>
<div class="line"><a name="l00433"></a><span class="lineno"> 433</span> }</div>
<div class="line"><a name="l00434"></a><span class="lineno"> 434</span> <span class="preprocessor">#endif</span></div>
<div class="ttc" id="classOpenMS_1_1ChromatogramPeak_html_a98fe0c3fba1788864d35d8ef6159459f"><div class="ttname"><a href="classOpenMS_1_1ChromatogramPeak.html#a98fe0c3fba1788864d35d8ef6159459f">OpenMS::ChromatogramPeak::setRT</a></div><div class="ttdeci">void setRT(CoordinateType rt)</div><div class="ttdoc">Mutable access to RT. </div><div class="ttdef"><b>Definition:</b> ChromatogramPeak.h:117</div></div>
<div class="ttc" id="classOpenMS_1_1CachedmzML_html_a8148ed639ab1958764997633934ddf38"><div class="ttname"><a href="classOpenMS_1_1CachedmzML.html#a8148ed639ab1958764997633934ddf38">OpenMS::CachedmzML::SpectrumType</a></div><div class="ttdeci">MSSpectrum< Peak1D > SpectrumType</div><div class="ttdef"><b>Definition:</b> CachedmzML.h:69</div></div>
<div class="ttc" id="Types_8h_html"><div class="ttname"><a href="Types_8h.html">Types.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="classOpenMS_1_1CachedmzML_html_ac37f5b61a6e64df22f26f98cd9f4f6d5"><div class="ttname"><a href="classOpenMS_1_1CachedmzML.html#ac37f5b61a6e64df22f26f98cd9f4f6d5">OpenMS::CachedmzML::createMemdumpIndex</a></div><div class="ttdeci">void createMemdumpIndex(String filename)</div><div class="ttdoc">Create an index on the location of all the spectra and chromatograms. </div><div class="ttdef"><b>Definition:</b> CachedmzML.h:217</div></div>
<div class="ttc" id="classOpenMS_1_1MSSpectrum_html_a1726d12d7597baa9fca0c1da0492f3da"><div class="ttname"><a href="classOpenMS_1_1MSSpectrum.html#a1726d12d7597baa9fca0c1da0492f3da">OpenMS::MSSpectrum::getMSLevel</a></div><div class="ttdeci">UInt getMSLevel() const </div><div class="ttdoc">Returns the MS level. </div><div class="ttdef"><b>Definition:</b> MSSpectrum.h:231</div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html_a9d78a687cf2a391198bb3cbc08bc06cb"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">OpenMS::MSExperiment::size</a></div><div class="ttdeci">Size size() const </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:117</div></div>
<div class="ttc" id="classOpenMS_1_1CachedmzML_html_a094c1fd87db598d60d692ed3f03547ba"><div class="ttname"><a href="classOpenMS_1_1CachedmzML.html#a094c1fd87db598d60d692ed3f03547ba">OpenMS::CachedmzML::spectra_index_</a></div><div class="ttdeci">std::vector< Size > spectra_index_</div><div class="ttdef"><b>Definition:</b> CachedmzML.h:429</div></div>
<div class="ttc" id="classOpenMS_1_1MSChromatogram_html"><div class="ttname"><a href="classOpenMS_1_1MSChromatogram.html">OpenMS::MSChromatogram</a></div><div class="ttdoc">The representation of a chromatogram. </div><div class="ttdef"><b>Definition:</b> MSChromatogram.h:53</div></div>
<div class="ttc" id="classOpenMS_1_1CachedmzML_html_af84b721d86630a1d8f05c4389070831b"><div class="ttname"><a href="classOpenMS_1_1CachedmzML.html#af84b721d86630a1d8f05c4389070831b">OpenMS::CachedmzML::writeChromatogram_</a></div><div class="ttdeci">void writeChromatogram_(const ChromatogramType &chromatogram, std::ofstream &ofs)</div><div class="ttdef"><b>Definition:</b> CachedmzML.h:414</div></div>
<div class="ttc" id="classOpenMS_1_1CachedmzML_html_acbe7ec10442c29895ba7b8881430b10c"><div class="ttname"><a href="classOpenMS_1_1CachedmzML.html#acbe7ec10442c29895ba7b8881430b10c">OpenMS::CachedmzML::DatumSingleton</a></div><div class="ttdeci">double DatumSingleton</div><div class="ttdef"><b>Definition:</b> CachedmzML.h:73</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_1CachedmzML_html_ae1739688d14fd48cfe0237b6033a56fc"><div class="ttname"><a href="classOpenMS_1_1CachedmzML.html#ae1739688d14fd48cfe0237b6033a56fc">OpenMS::CachedmzML::readSingleSpectrum</a></div><div class="ttdeci">void readSingleSpectrum(MSSpectrum< Peak1D > &spectrum, std::ifstream &ifs, const Size &idx) const </div><div class="ttdef"><b>Definition:</b> CachedmzML.h:192</div></div>
<div class="ttc" id="classOpenMS_1_1CachedmzML_html_acc92c018e6237189da684e845d9b5f9d"><div class="ttname"><a href="classOpenMS_1_1CachedmzML.html#acc92c018e6237189da684e845d9b5f9d">OpenMS::CachedmzML::ChromatogramType</a></div><div class="ttdeci">MSChromatogram< ChromatogramPeak > ChromatogramType</div><div class="ttdef"><b>Definition:</b> CachedmzML.h:70</div></div>
<div class="ttc" id="classOpenMS_1_1CachedmzML_html_ab52083d2b64e8db5b7a61c399e288859"><div class="ttname"><a href="classOpenMS_1_1CachedmzML.html#ab52083d2b64e8db5b7a61c399e288859">OpenMS::CachedmzML::MapType</a></div><div class="ttdeci">MSExperiment< Peak1D > MapType</div><div class="ttdef"><b>Definition:</b> CachedmzML.h:68</div></div>
<div class="ttc" id="classdouble_html"><div class="ttname"><a href="classdouble.html">double</a></div></div>
<div class="ttc" id="classOpenMS_1_1Peak1D_html_ab9c4ce5d172a75d6de2c6f5f1847c9ab"><div class="ttname"><a href="classOpenMS_1_1Peak1D.html#ab9c4ce5d172a75d6de2c6f5f1847c9ab">OpenMS::Peak1D::setMZ</a></div><div class="ttdeci">void setMZ(CoordinateType mz)</div><div class="ttdoc">Mutable access to m/z. </div><div class="ttdef"><b>Definition:</b> Peak1D.h:114</div></div>
<div class="ttc" id="classOpenMS_1_1Peak1D_html_ab875c2479c6cd2a0189e4684bfa4f97d"><div class="ttname"><a href="classOpenMS_1_1Peak1D.html#ab875c2479c6cd2a0189e4684bfa4f97d">OpenMS::Peak1D::setIntensity</a></div><div class="ttdeci">void setIntensity(IntensityType intensity)</div><div class="ttdoc">Mutable access to the data point intensity (height) </div><div class="ttdef"><b>Definition:</b> Peak1D.h:105</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="MSExperiment_8h_html"><div class="ttname"><a href="MSExperiment_8h.html">MSExperiment.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1CachedmzML_html_a3dc2908daf773558c67dca821c1d0ae7"><div class="ttname"><a href="classOpenMS_1_1CachedmzML.html#a3dc2908daf773558c67dca821c1d0ae7">OpenMS::CachedmzML::readChromatogram_</a></div><div class="ttdeci">void readChromatogram_(ChromatogramType &chromatogram, std::ifstream &ifs) const </div><div class="ttdef"><b>Definition:</b> CachedmzML.h:369</div></div>
<div class="ttc" id="classOpenMS_1_1MSSpectrum_html"><div class="ttname"><a href="classOpenMS_1_1MSSpectrum.html">OpenMS::MSSpectrum< Peak1D ></a></div></div>
<div class="ttc" id="classOpenMS_1_1CachedmzML_html_a78668c2f83b7e9e4fe595c57ab4c642d"><div class="ttname"><a href="classOpenMS_1_1CachedmzML.html#a78668c2f83b7e9e4fe595c57ab4c642d">OpenMS::CachedmzML::readMemdump</a></div><div class="ttdeci">void readMemdump(MapType &exp_reading, String filename) const </div><div class="ttdoc">Read all spectra from a dump from the disk. </div><div class="ttdef"><b>Definition:</b> CachedmzML.h:139</div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html_af5e67d26823ec12e91434f4e74faa9d1"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html#af5e67d26823ec12e91434f4e74faa9d1">OpenMS::MSExperiment::reserve</a></div><div class="ttdeci">void reserve(Size s)</div><div class="ttdef"><b>Definition:</b> MSExperiment.h:132</div></div>
<div class="ttc" id="classOpenMS_1_1CachedmzML_html_adde8fb22b8fbfc4d985d8a8467ad91f5"><div class="ttname"><a href="classOpenMS_1_1CachedmzML.html#adde8fb22b8fbfc4d985d8a8467ad91f5">OpenMS::CachedmzML::getSpectraIndex</a></div><div class="ttdeci">const std::vector< Size > & getSpectraIndex() const </div><div class="ttdef"><b>Definition:</b> CachedmzML.h:204</div></div>
<div class="ttc" id="classOpenMS_1_1CachedmzML_html_a608b23b52372613ab1bcbd1ef741a8e9"><div class="ttname"><a href="classOpenMS_1_1CachedmzML.html#a608b23b52372613ab1bcbd1ef741a8e9">OpenMS::CachedmzML::operator=</a></div><div class="ttdeci">CachedmzML & operator=(const CachedmzML &rhs)</div><div class="ttdoc">Assignment operator. </div><div class="ttdef"><b>Definition:</b> CachedmzML.h:94</div></div>
<div class="ttc" id="classOpenMS_1_1Peak1D_html"><div class="ttname"><a href="classOpenMS_1_1Peak1D.html">OpenMS::Peak1D</a></div><div class="ttdoc">A 1-dimensional raw data point or peak. </div><div class="ttdef"><b>Definition:</b> Peak1D.h:55</div></div>
<div class="ttc" id="classOpenMS_1_1MSSpectrum_html_a24f081fe74bbbf773533ad19e96d8358"><div class="ttname"><a href="classOpenMS_1_1MSSpectrum.html#a24f081fe74bbbf773533ad19e96d8358">OpenMS::MSSpectrum::setMSLevel</a></div><div class="ttdeci">void setMSLevel(UInt ms_level)</div><div class="ttdoc">Sets the MS level. </div><div class="ttdef"><b>Definition:</b> MSSpectrum.h:237</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_1CachedmzML_html_a4a462892f19dc42bfeb2f1b67098eba9"><div class="ttname"><a href="classOpenMS_1_1CachedmzML.html#a4a462892f19dc42bfeb2f1b67098eba9">OpenMS::CachedmzML::getChromatogramIndex</a></div><div class="ttdeci">const std::vector< Size > & getChromatogramIndex() const </div><div class="ttdef"><b>Definition:</b> CachedmzML.h:209</div></div>
<div class="ttc" id="namespaceOpenSwath_html_a8aaa5999a567d0b9a393ea480244162b"><div class="ttname"><a href="namespaceOpenSwath.html#a8aaa5999a567d0b9a393ea480244162b">OpenSwath::BinaryDataArrayPtr</a></div><div class="ttdeci">OPENSWATHALGO_DLLAPI typedef boost::shared_ptr< BinaryDataArray > BinaryDataArrayPtr</div><div class="ttdef"><b>Definition:</b> ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:77</div></div>
<div class="ttc" id="classOpenMS_1_1CachedmzML_html_a18bb8f03c608ff0936723df34eef1e2c"><div class="ttname"><a href="classOpenMS_1_1CachedmzML.html#a18bb8f03c608ff0936723df34eef1e2c">OpenMS::CachedmzML::Datavector</a></div><div class="ttdeci">std::vector< DatumSingleton > Datavector</div><div class="ttdef"><b>Definition:</b> CachedmzML.h:78</div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html_ae9dafbb74a1a4c430ceef03e25ab8e10"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html#ae9dafbb74a1a4c430ceef03e25ab8e10">OpenMS::MSExperiment::addSpectrum</a></div><div class="ttdeci">void addSpectrum(const MSSpectrum< PeakT > &spectrum)</div><div class="ttdoc">adds a spectra to the list </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:738</div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html">OpenMS::MSExperiment< Peak1D ></a></div></div>
<div class="ttc" id="CachedmzML_8h_html_a54061e5993a5517320d425f44408cc86"><div class="ttname"><a href="CachedmzML_8h.html#a54061e5993a5517320d425f44408cc86">MAGIC_NUMBER</a></div><div class="ttdeci">#define MAGIC_NUMBER</div><div class="ttdef"><b>Definition:</b> CachedmzML.h:48</div></div>
<div class="ttc" id="classOpenMS_1_1CachedmzML_html_a357a85b39a2e70c765e95f12cf46579c"><div class="ttname"><a href="classOpenMS_1_1CachedmzML.html#a357a85b39a2e70c765e95f12cf46579c">OpenMS::CachedmzML::readSpectrum_</a></div><div class="ttdeci">void readSpectrum_(SpectrumType &spectrum, std::ifstream &ifs) const </div><div class="ttdef"><b>Definition:</b> CachedmzML.h:346</div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html_a4c105ad43f3c61a53997af8ba28720e2"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html#a4c105ad43f3c61a53997af8ba28720e2">OpenMS::MSExperiment::setChromatograms</a></div><div class="ttdeci">void setChromatograms(const std::vector< MSChromatogram< ChromatogramPeakType > > &chromatograms)</div><div class="ttdoc">sets the chromatogram list </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:756</div></div>
<div class="ttc" id="classOpenMS_1_1CachedmzML_html_a898c0cb00444946a2de2e4c77b0c3d17"><div class="ttname"><a href="classOpenMS_1_1CachedmzML.html#a898c0cb00444946a2de2e4c77b0c3d17">OpenMS::CachedmzML::writeSpectrum_</a></div><div class="ttdeci">void writeSpectrum_(const SpectrumType &spectrum, std::ofstream &ofs)</div><div class="ttdef"><b>Definition:</b> CachedmzML.h:387</div></div>
<div class="ttc" id="classOpenMS_1_1ChromatogramPeak_html_ab875c2479c6cd2a0189e4684bfa4f97d"><div class="ttname"><a href="classOpenMS_1_1ChromatogramPeak.html#ab875c2479c6cd2a0189e4684bfa4f97d">OpenMS::ChromatogramPeak::setIntensity</a></div><div class="ttdeci">void setIntensity(IntensityType intensity)</div><div class="ttdoc">Mutable access to the data point intensity (height) </div><div class="ttdef"><b>Definition:</b> ChromatogramPeak.h:108</div></div>
<div class="ttc" id="classOpenMS_1_1MSSpectrum_html_aac8c50f318154e9e5b7b01aee806e17f"><div class="ttname"><a href="classOpenMS_1_1MSSpectrum.html#aac8c50f318154e9e5b7b01aee806e17f">OpenMS::MSSpectrum::setRT</a></div><div class="ttdeci">void setRT(DoubleReal rt)</div><div class="ttdoc">Sets the absolute retention time (is seconds) </div><div class="ttdef"><b>Definition:</b> MSSpectrum.h:221</div></div>
<div class="ttc" id="classOpenMS_1_1CachedmzML_html"><div class="ttname"><a href="classOpenMS_1_1CachedmzML.html">OpenMS::CachedmzML</a></div><div class="ttdoc">An class that uses on-disk caching to read and write spectra and chromatograms. </div><div class="ttdef"><b>Definition:</b> CachedmzML.h:60</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_1CachedmzML_html_a5fe3a9e1e476192f7f0e9818cbce3ceb"><div class="ttname"><a href="classOpenMS_1_1CachedmzML.html#a5fe3a9e1e476192f7f0e9818cbce3ceb">OpenMS::CachedmzML::readChromatogramFast</a></div><div class="ttdeci">static void readChromatogramFast(OpenSwath::BinaryDataArrayPtr data1, OpenSwath::BinaryDataArrayPtr data2, std::ifstream &ifs)</div><div class="ttdoc">fast access without copying </div><div class="ttdef"><b>Definition:</b> CachedmzML.h:306</div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html_af072fc84225ae927f7527f208ea86cbd"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html#af072fc84225ae927f7527f208ea86cbd">OpenMS::MSExperiment::clear</a></div><div class="ttdeci">void clear(bool clear_meta_data)</div><div class="ttdoc">Clears all data and meta data. </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:809</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_1CachedmzML_html_afc7807c8e8c717754f5355d4a85e8ea2"><div class="ttname"><a href="classOpenMS_1_1CachedmzML.html#afc7807c8e8c717754f5355d4a85e8ea2">OpenMS::CachedmzML::readSpectrumFast</a></div><div class="ttdeci">static void readSpectrumFast(OpenSwath::BinaryDataArrayPtr data1, OpenSwath::BinaryDataArrayPtr data2, std::ifstream &ifs, int ms_level, double rt)</div><div class="ttdoc">fast access without copying </div><div class="ttdef"><b>Definition:</b> CachedmzML.h:290</div></div>
<div class="ttc" id="classOpenMS_1_1CachedmzML_html_aeef724ccc70a46b7a027d2f0db112ea0"><div class="ttname"><a href="classOpenMS_1_1CachedmzML.html#aeef724ccc70a46b7a027d2f0db112ea0">OpenMS::CachedmzML::readSpectrum_</a></div><div class="ttdeci">void readSpectrum_(Datavector &data1, Datavector &data2, std::ifstream &ifs, int &ms_level, double &rt) const </div><div class="ttdef"><b>Definition:</b> CachedmzML.h:321</div></div>
<div class="ttc" id="classOpenMS_1_1CachedmzML_html_aaaf884a9b63880d037ee5aab0115b567"><div class="ttname"><a href="classOpenMS_1_1CachedmzML.html#aaaf884a9b63880d037ee5aab0115b567">OpenMS::CachedmzML::dbl_field_</a></div><div class="ttdeci">double dbl_field_</div><div class="ttdef"><b>Definition:</b> CachedmzML.h:64</div></div>
<div class="ttc" id="classOpenMS_1_1ChromatogramPeak_html"><div class="ttname"><a href="classOpenMS_1_1ChromatogramPeak.html">OpenMS::ChromatogramPeak</a></div><div class="ttdoc">A 1-dimensional raw data point or peak for chromatograms. </div><div class="ttdef"><b>Definition:</b> ChromatogramPeak.h:55</div></div>
<div class="ttc" id="classOpenMS_1_1CachedmzML_html_a310dba1a46765ac74b704cfebb30a1ef"><div class="ttname"><a href="classOpenMS_1_1CachedmzML.html#a310dba1a46765ac74b704cfebb30a1ef">OpenMS::CachedmzML::int_field_</a></div><div class="ttdeci">int int_field_</div><div class="ttdef"><b>Definition:</b> CachedmzML.h:63</div></div>
<div class="ttc" id="ANALYSIS_2OPENSWATH_2OPENSWATHALGO_2DATAACCESS_2ISpectrumAccess_8h_html"><div class="ttname"><a href="ANALYSIS_2OPENSWATH_2OPENSWATHALGO_2DATAACCESS_2ISpectrumAccess_8h.html">ISpectrumAccess.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1CachedmzML_html_ad4ab33d391cc72c4b5e1720588a41958"><div class="ttname"><a href="classOpenMS_1_1CachedmzML.html#ad4ab33d391cc72c4b5e1720588a41958">OpenMS::CachedmzML::readChromatogram_</a></div><div class="ttdeci">void readChromatogram_(Datavector &data1, Datavector &data2, std::ifstream &ifs) const </div><div class="ttdef"><b>Definition:</b> CachedmzML.h:335</div></div>
<div class="ttc" id="classOpenMS_1_1MSSpectrum_html_a3da529bd3240fa0d7148484bbef0b9d7"><div class="ttname"><a href="classOpenMS_1_1MSSpectrum.html#a3da529bd3240fa0d7148484bbef0b9d7">OpenMS::MSSpectrum::getRT</a></div><div class="ttdeci">DoubleReal getRT() const </div><div class="ttdef"><b>Definition:</b> MSSpectrum.h:215</div></div>
<div class="ttc" id="classOpenMS_1_1CachedmzML_html_a15d13796ad38b3a74526f89cc6b07f01"><div class="ttname"><a href="classOpenMS_1_1CachedmzML.html#a15d13796ad38b3a74526f89cc6b07f01">OpenMS::CachedmzML::chrom_index_</a></div><div class="ttdeci">std::vector< Size > chrom_index_</div><div class="ttdef"><b>Definition:</b> CachedmzML.h:430</div></div>
<div class="ttc" id="classOpenMS_1_1CachedmzML_html_afe7d98074c75e0f8a4f47299fdebf34e"><div class="ttname"><a href="classOpenMS_1_1CachedmzML.html#afe7d98074c75e0f8a4f47299fdebf34e">OpenMS::CachedmzML::~CachedmzML</a></div><div class="ttdeci">~CachedmzML()</div><div class="ttdoc">Default destructor. </div><div class="ttdef"><b>Definition:</b> CachedmzML.h:89</div></div>
<div class="ttc" id="classOpenMS_1_1CachedmzML_html_ad117b85f93b2c7c04b5031c4d6f70a9f"><div class="ttname"><a href="classOpenMS_1_1CachedmzML.html#ad117b85f93b2c7c04b5031c4d6f70a9f">OpenMS::CachedmzML::writeMetadata</a></div><div class="ttdeci">void writeMetadata(MapType exp, String out_meta)</div><div class="ttdoc">Write only the meta data of an MSExperiment. </div><div class="ttdef"><b>Definition:</b> CachedmzML.h:268</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="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>
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