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<a href="MascotInfile_8h.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno">    1</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00002"></a><span class="lineno">    2</span>&#160;<span class="comment">//                   OpenMS -- Open-Source Mass Spectrometry</span></div>
<div class="line"><a name="l00003"></a><span class="lineno">    3</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00004"></a><span class="lineno">    4</span>&#160;<span class="comment">// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,</span></div>
<div class="line"><a name="l00005"></a><span class="lineno">    5</span>&#160;<span class="comment">// ETH Zurich, and Freie Universitaet Berlin 2002-2013.</span></div>
<div class="line"><a name="l00006"></a><span class="lineno">    6</span>&#160;<span class="comment">//</span></div>
<div class="line"><a name="l00007"></a><span class="lineno">    7</span>&#160;<span class="comment">// This software is released under a three-clause BSD license:</span></div>
<div class="line"><a name="l00008"></a><span class="lineno">    8</span>&#160;<span class="comment">//  * Redistributions of source code must retain the above copyright</span></div>
<div class="line"><a name="l00009"></a><span class="lineno">    9</span>&#160;<span class="comment">//    notice, this list of conditions and the following disclaimer.</span></div>
<div class="line"><a name="l00010"></a><span class="lineno">   10</span>&#160;<span class="comment">//  * Redistributions in binary form must reproduce the above copyright</span></div>
<div class="line"><a name="l00011"></a><span class="lineno">   11</span>&#160;<span class="comment">//    notice, this list of conditions and the following disclaimer in the</span></div>
<div class="line"><a name="l00012"></a><span class="lineno">   12</span>&#160;<span class="comment">//    documentation and/or other materials provided with the distribution.</span></div>
<div class="line"><a name="l00013"></a><span class="lineno">   13</span>&#160;<span class="comment">//  * Neither the name of any author or any participating institution</span></div>
<div class="line"><a name="l00014"></a><span class="lineno">   14</span>&#160;<span class="comment">//    may be used to endorse or promote products derived from this software</span></div>
<div class="line"><a name="l00015"></a><span class="lineno">   15</span>&#160;<span class="comment">//    without specific prior written permission.</span></div>
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<div class="line"><a name="l00017"></a><span class="lineno">   17</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00018"></a><span class="lineno">   18</span>&#160;<span class="comment">// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS &quot;AS IS&quot;</span></div>
<div class="line"><a name="l00019"></a><span class="lineno">   19</span>&#160;<span class="comment">// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE</span></div>
<div class="line"><a name="l00020"></a><span class="lineno">   20</span>&#160;<span class="comment">// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE</span></div>
<div class="line"><a name="l00021"></a><span class="lineno">   21</span>&#160;<span class="comment">// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING</span></div>
<div class="line"><a name="l00022"></a><span class="lineno">   22</span>&#160;<span class="comment">// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,</span></div>
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<div class="line"><a name="l00027"></a><span class="lineno">   27</span>&#160;<span class="comment">// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF</span></div>
<div class="line"><a name="l00028"></a><span class="lineno">   28</span>&#160;<span class="comment">// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</span></div>
<div class="line"><a name="l00029"></a><span class="lineno">   29</span>&#160;<span class="comment">//</span></div>
<div class="line"><a name="l00030"></a><span class="lineno">   30</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00031"></a><span class="lineno">   31</span>&#160;<span class="comment">// $Maintainer: Nico Pfeifer $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160;<span class="comment">// $Authors: $</span></div>
<div class="line"><a name="l00033"></a><span class="lineno">   33</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00034"></a><span class="lineno">   34</span>&#160;</div>
<div class="line"><a name="l00035"></a><span class="lineno">   35</span>&#160;<span class="preprocessor">#ifndef OPENMS_FORMAT_MASCOTINFILE_H</span></div>
<div class="line"><a name="l00036"></a><span class="lineno">   36</span>&#160;<span class="preprocessor"></span><span class="preprocessor">#define OPENMS_FORMAT_MASCOTINFILE_H</span></div>
<div class="line"><a name="l00037"></a><span class="lineno">   37</span>&#160;<span class="preprocessor"></span></div>
<div class="line"><a name="l00038"></a><span class="lineno">   38</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="MSExperiment_8h.html">OpenMS/KERNEL/MSExperiment.h</a>&gt;</span></div>
<div class="line"><a name="l00039"></a><span class="lineno">   39</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="String_8h.html">OpenMS/DATASTRUCTURES/String.h</a>&gt;</span></div>
<div class="line"><a name="l00040"></a><span class="lineno">   40</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="File_8h.html">OpenMS/SYSTEM/File.h</a>&gt;</span></div>
<div class="line"><a name="l00041"></a><span class="lineno">   41</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="ProgressLogger_8h.html">OpenMS/CONCEPT/ProgressLogger.h</a>&gt;</span></div>
<div class="line"><a name="l00042"></a><span class="lineno">   42</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="StandardTypes_8h.html">OpenMS/KERNEL/StandardTypes.h</a>&gt;</span></div>
<div class="line"><a name="l00043"></a><span class="lineno">   43</span>&#160;</div>
<div class="line"><a name="l00044"></a><span class="lineno">   44</span>&#160;<span class="preprocessor">#include &lt;vector&gt;</span></div>
<div class="line"><a name="l00045"></a><span class="lineno">   45</span>&#160;<span class="preprocessor">#include &lt;fstream&gt;</span></div>
<div class="line"><a name="l00046"></a><span class="lineno">   46</span>&#160;</div>
<div class="line"><a name="l00047"></a><span class="lineno">   47</span>&#160;<span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00048"></a><span class="lineno">   48</span>&#160;{</div>
<div class="line"><a name="l00059"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MascotInfile.html">   59</a></span>&#160;  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1MascotInfile.html">MascotInfile</a> :</div>
<div class="line"><a name="l00060"></a><span class="lineno">   60</span>&#160;    <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a></div>
<div class="line"><a name="l00061"></a><span class="lineno">   61</span>&#160;  {</div>
<div class="line"><a name="l00062"></a><span class="lineno">   62</span>&#160;<span class="keyword">public</span>:</div>
<div class="line"><a name="l00063"></a><span class="lineno">   63</span>&#160;</div>
<div class="line"><a name="l00065"></a><span class="lineno">   65</span>&#160;    <a class="code" href="classOpenMS_1_1MascotInfile.html">MascotInfile</a>();</div>
<div class="line"><a name="l00066"></a><span class="lineno">   66</span>&#160;</div>
<div class="line"><a name="l00068"></a><span class="lineno">   68</span>&#160;    <span class="keyword">virtual</span> ~<a class="code" href="classOpenMS_1_1MascotInfile.html">MascotInfile</a>();</div>
<div class="line"><a name="l00069"></a><span class="lineno">   69</span>&#160;</div>
<div class="line"><a name="l00071"></a><span class="lineno">   71</span>&#160;    <span class="keywordtype">void</span> store(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; filename, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html">PeakSpectrum</a> &amp; spec, <a class="code" href="classdouble.html">DoubleReal</a> mz, <a class="code" href="classdouble.html">DoubleReal</a> retention_time, <a class="code" href="classOpenMS_1_1String.html">String</a> search_title);</div>
<div class="line"><a name="l00072"></a><span class="lineno">   72</span>&#160;</div>
<div class="line"><a name="l00074"></a><span class="lineno">   74</span>&#160;    <span class="keywordtype">void</span> store(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; filename, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment&lt;&gt;</a> &amp; experiment, <a class="code" href="classOpenMS_1_1String.html">String</a> search_title);</div>
<div class="line"><a name="l00075"></a><span class="lineno">   75</span>&#160;</div>
<div class="line"><a name="l00082"></a><span class="lineno">   82</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">typename</span> MapType&gt;</div>
<div class="line"><a name="l00083"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MascotInfile.html#a98bebe67b8b06a9a67a3654d631355b4">   83</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1MascotInfile.html#a98bebe67b8b06a9a67a3654d631355b4">load</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; filename, MapType &amp; exp)</div>
<div class="line"><a name="l00084"></a><span class="lineno">   84</span>&#160;    {</div>
<div class="line"><a name="l00085"></a><span class="lineno">   85</span>&#160;      exp.reset();</div>
<div class="line"><a name="l00086"></a><span class="lineno">   86</span>&#160;      <span class="keywordflow">if</span> (!<a class="code" href="classOpenMS_1_1File.html#a103bc592f26fed81f56f2f92b7ab5063">File::exists</a>(filename))</div>
<div class="line"><a name="l00087"></a><span class="lineno">   87</span>&#160;      {</div>
<div class="line"><a name="l00088"></a><span class="lineno">   88</span>&#160;        <span class="keywordflow">throw</span> <a class="code" href="classOpenMS_1_1Exception_1_1FileNotFound.html">Exception::FileNotFound</a>(__FILE__, __LINE__, __PRETTY_FUNCTION__, filename);</div>
<div class="line"><a name="l00089"></a><span class="lineno">   89</span>&#160;      }</div>
<div class="line"><a name="l00090"></a><span class="lineno">   90</span>&#160;</div>
<div class="line"><a name="l00091"></a><span class="lineno">   91</span>&#160;      std::ifstream is(filename.c_str());</div>
<div class="line"><a name="l00092"></a><span class="lineno">   92</span>&#160;      std::vector&lt;std::pair&lt;double, double&gt; &gt; spec;</div>
<div class="line"><a name="l00093"></a><span class="lineno">   93</span>&#160;      <a class="code" href="classunsigned_01int.html">UInt</a> charge(0);</div>
<div class="line"><a name="l00094"></a><span class="lineno">   94</span>&#160;      <span class="keywordtype">double</span> pre_mz(0), pre_int(0), rt(-1);</div>
<div class="line"><a name="l00095"></a><span class="lineno">   95</span>&#160;      <a class="code" href="classOpenMS_1_1String.html">String</a> title;</div>
<div class="line"><a name="l00096"></a><span class="lineno">   96</span>&#160;      <span class="keywordflow">while</span> (getNextSpectrum_(is, spec, charge, pre_mz, pre_int, rt, title))</div>
<div class="line"><a name="l00097"></a><span class="lineno">   97</span>&#160;      {</div>
<div class="line"><a name="l00098"></a><span class="lineno">   98</span>&#160;        <span class="keyword">typename</span> MapType::SpectrumType spectrum;</div>
<div class="line"><a name="l00099"></a><span class="lineno">   99</span>&#160;        <span class="keywordflow">for</span> (std::vector&lt;std::pair&lt;double, double&gt; &gt;::const_iterator it = spec.begin(); it != spec.end(); ++it)</div>
<div class="line"><a name="l00100"></a><span class="lineno">  100</span>&#160;        {</div>
<div class="line"><a name="l00101"></a><span class="lineno">  101</span>&#160;          <span class="keyword">typename</span> <a class="code" href="namespaceOpenMS.html#a013338b7bdbb5c3b4c78666656070e23">MapType::PeakType</a> p;</div>
<div class="line"><a name="l00102"></a><span class="lineno">  102</span>&#160;          p.<a class="code" href="classOpenMS_1_1Peak2D.html#abbdecccbbcf763c6c5eae3b7c3cb915e">setPosition</a>(it-&gt;first);</div>
<div class="line"><a name="l00103"></a><span class="lineno">  103</span>&#160;          p.setIntensity(it-&gt;second);</div>
<div class="line"><a name="l00104"></a><span class="lineno">  104</span>&#160;          spectrum.push_back(p);</div>
<div class="line"><a name="l00105"></a><span class="lineno">  105</span>&#160;        }</div>
<div class="line"><a name="l00106"></a><span class="lineno">  106</span>&#160;        spectrum.setMSLevel(2);</div>
<div class="line"><a name="l00107"></a><span class="lineno">  107</span>&#160;        spectrum.getPrecursors().resize(1);</div>
<div class="line"><a name="l00108"></a><span class="lineno">  108</span>&#160;        spectrum.getPrecursors()[0].setMZ(pre_mz);</div>
<div class="line"><a name="l00109"></a><span class="lineno">  109</span>&#160;        spectrum.getPrecursors()[0].setIntensity(pre_int);</div>
<div class="line"><a name="l00110"></a><span class="lineno">  110</span>&#160;        spectrum.getPrecursors()[0].setCharge(charge);</div>
<div class="line"><a name="l00111"></a><span class="lineno">  111</span>&#160;        spectrum.setRT(rt);</div>
<div class="line"><a name="l00112"></a><span class="lineno">  112</span>&#160;        <span class="keywordflow">if</span> (title != <span class="stringliteral">&quot;&quot;</span>)</div>
<div class="line"><a name="l00113"></a><span class="lineno">  113</span>&#160;        {</div>
<div class="line"><a name="l00114"></a><span class="lineno">  114</span>&#160;          spectrum.setMetaValue(<span class="stringliteral">&quot;TITLE&quot;</span>, title);</div>
<div class="line"><a name="l00115"></a><span class="lineno">  115</span>&#160;          title = <span class="stringliteral">&quot;&quot;</span>;</div>
<div class="line"><a name="l00116"></a><span class="lineno">  116</span>&#160;        }</div>
<div class="line"><a name="l00117"></a><span class="lineno">  117</span>&#160;</div>
<div class="line"><a name="l00118"></a><span class="lineno">  118</span>&#160;        exp.addSpectrum(spectrum);</div>
<div class="line"><a name="l00119"></a><span class="lineno">  119</span>&#160;</div>
<div class="line"><a name="l00120"></a><span class="lineno">  120</span>&#160;        <span class="comment">// clean up</span></div>
<div class="line"><a name="l00121"></a><span class="lineno">  121</span>&#160;        spec.clear();</div>
<div class="line"><a name="l00122"></a><span class="lineno">  122</span>&#160;        charge = 0;</div>
<div class="line"><a name="l00123"></a><span class="lineno">  123</span>&#160;        pre_mz = 0;</div>
<div class="line"><a name="l00124"></a><span class="lineno">  124</span>&#160;        pre_int = 0;</div>
<div class="line"><a name="l00125"></a><span class="lineno">  125</span>&#160;      }</div>
<div class="line"><a name="l00126"></a><span class="lineno">  126</span>&#160;    }</div>
<div class="line"><a name="l00127"></a><span class="lineno">  127</span>&#160;</div>
<div class="line"><a name="l00129"></a><span class="lineno">  129</span>&#160;    <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; getBoundary();</div>
<div class="line"><a name="l00131"></a><span class="lineno">  131</span>&#160;    <span class="keywordtype">void</span> setBoundary(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; boundary);</div>
<div class="line"><a name="l00132"></a><span class="lineno">  132</span>&#160;</div>
<div class="line"><a name="l00134"></a><span class="lineno">  134</span>&#160;    <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; getDB();</div>
<div class="line"><a name="l00136"></a><span class="lineno">  136</span>&#160;    <span class="keywordtype">void</span> setDB(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; db);</div>
<div class="line"><a name="l00137"></a><span class="lineno">  137</span>&#160;</div>
<div class="line"><a name="l00139"></a><span class="lineno">  139</span>&#160;    <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; getSearchType();</div>
<div class="line"><a name="l00141"></a><span class="lineno">  141</span>&#160;    <span class="keywordtype">void</span> setSearchType(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; search_type);</div>
<div class="line"><a name="l00142"></a><span class="lineno">  142</span>&#160;</div>
<div class="line"><a name="l00144"></a><span class="lineno">  144</span>&#160;    <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; getHits();</div>
<div class="line"><a name="l00146"></a><span class="lineno">  146</span>&#160;    <span class="keywordtype">void</span> setHits(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; hits);</div>
<div class="line"><a name="l00147"></a><span class="lineno">  147</span>&#160;</div>
<div class="line"><a name="l00149"></a><span class="lineno">  149</span>&#160;    <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; getCleavage();</div>
<div class="line"><a name="l00151"></a><span class="lineno">  151</span>&#160;    <span class="keywordtype">void</span> setCleavage(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; cleavage);</div>
<div class="line"><a name="l00152"></a><span class="lineno">  152</span>&#160;</div>
<div class="line"><a name="l00154"></a><span class="lineno">  154</span>&#160;    <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; getMassType();</div>
<div class="line"><a name="l00156"></a><span class="lineno">  156</span>&#160;    <span class="keywordtype">void</span> setMassType(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; mass_type);</div>
<div class="line"><a name="l00157"></a><span class="lineno">  157</span>&#160;</div>
<div class="line"><a name="l00159"></a><span class="lineno">  159</span>&#160;    <span class="keyword">const</span> std::vector&lt;String&gt; &amp; getModifications();</div>
<div class="line"><a name="l00161"></a><span class="lineno">  161</span>&#160;    <span class="keywordtype">void</span> setModifications(<span class="keyword">const</span> std::vector&lt;String&gt; &amp; mods);</div>
<div class="line"><a name="l00162"></a><span class="lineno">  162</span>&#160;</div>
<div class="line"><a name="l00164"></a><span class="lineno">  164</span>&#160;    <span class="keyword">const</span> std::vector&lt;String&gt; &amp; getVariableModifications();</div>
<div class="line"><a name="l00166"></a><span class="lineno">  166</span>&#160;    <span class="keywordtype">void</span> setVariableModifications(<span class="keyword">const</span> std::vector&lt;String&gt; &amp; mods);</div>
<div class="line"><a name="l00167"></a><span class="lineno">  167</span>&#160;</div>
<div class="line"><a name="l00169"></a><span class="lineno">  169</span>&#160;    <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; getInstrument();</div>
<div class="line"><a name="l00171"></a><span class="lineno">  171</span>&#160;    <span class="keywordtype">void</span> setInstrument(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; instrument);</div>
<div class="line"><a name="l00172"></a><span class="lineno">  172</span>&#160;</div>
<div class="line"><a name="l00174"></a><span class="lineno">  174</span>&#160;    <a class="code" href="classunsigned_01int.html">UInt</a> getMissedCleavages();</div>
<div class="line"><a name="l00176"></a><span class="lineno">  176</span>&#160;    <span class="keywordtype">void</span> setMissedCleavages(<a class="code" href="classunsigned_01int.html">UInt</a> missed_cleavages);</div>
<div class="line"><a name="l00177"></a><span class="lineno">  177</span>&#160;</div>
<div class="line"><a name="l00179"></a><span class="lineno">  179</span>&#160;    <a class="code" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a> getPrecursorMassTolerance();</div>
<div class="line"><a name="l00181"></a><span class="lineno">  181</span>&#160;    <span class="keywordtype">void</span> setPrecursorMassTolerance(<a class="code" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a> precursor_mass_tolerance);</div>
<div class="line"><a name="l00182"></a><span class="lineno">  182</span>&#160;</div>
<div class="line"><a name="l00184"></a><span class="lineno">  184</span>&#160;    <a class="code" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a> getPeakMassTolerance();</div>
<div class="line"><a name="l00186"></a><span class="lineno">  186</span>&#160;    <span class="keywordtype">void</span> setPeakMassTolerance(<a class="code" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a> ion_mass_tolerance);</div>
<div class="line"><a name="l00187"></a><span class="lineno">  187</span>&#160;</div>
<div class="line"><a name="l00189"></a><span class="lineno">  189</span>&#160;    <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; getTaxonomy();</div>
<div class="line"><a name="l00191"></a><span class="lineno">  191</span>&#160;    <span class="keywordtype">void</span> setTaxonomy(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; taxonomy);</div>
<div class="line"><a name="l00192"></a><span class="lineno">  192</span>&#160;</div>
<div class="line"><a name="l00194"></a><span class="lineno">  194</span>&#160;    <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; getFormVersion();</div>
<div class="line"><a name="l00196"></a><span class="lineno">  196</span>&#160;    <span class="keywordtype">void</span> setFormVersion(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; form_version);</div>
<div class="line"><a name="l00197"></a><span class="lineno">  197</span>&#160;</div>
<div class="line"><a name="l00199"></a><span class="lineno">  199</span>&#160;    <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; getCharges();</div>
<div class="line"><a name="l00201"></a><span class="lineno">  201</span>&#160;    <span class="keywordtype">void</span> setCharges(std::vector&lt;Int&gt; &amp; charges);</div>
<div class="line"><a name="l00202"></a><span class="lineno">  202</span>&#160;</div>
<div class="line"><a name="l00203"></a><span class="lineno">  203</span>&#160;<span class="keyword">protected</span>:</div>
<div class="line"><a name="l00205"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MascotInfile.html#ae23f3c856a76faaa8a37015bd7fef8bc">  205</a></span>&#160;    <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1MascotInfile.html#ae23f3c856a76faaa8a37015bd7fef8bc">mz_</a>;</div>
<div class="line"><a name="l00206"></a><span class="lineno">  206</span>&#160;</div>
<div class="line"><a name="l00208"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MascotInfile.html#afc5f9aaffcc298be4bd38a79480ed304">  208</a></span>&#160;    <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1MascotInfile.html#afc5f9aaffcc298be4bd38a79480ed304">charges_</a>;</div>
<div class="line"><a name="l00209"></a><span class="lineno">  209</span>&#160;</div>
<div class="line"><a name="l00211"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MascotInfile.html#a41ab11ce76df5f4c9eb364c63d7e6eba">  211</a></span>&#160;    <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1MascotInfile.html#a41ab11ce76df5f4c9eb364c63d7e6eba">search_title_</a>;</div>
<div class="line"><a name="l00212"></a><span class="lineno">  212</span>&#160;</div>
<div class="line"><a name="l00214"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MascotInfile.html#a488bf544f6efc29a3265943c28aba0f2">  214</a></span>&#160;    <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1MascotInfile.html#a488bf544f6efc29a3265943c28aba0f2">db_</a>;</div>
<div class="line"><a name="l00215"></a><span class="lineno">  215</span>&#160;</div>
<div class="line"><a name="l00217"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MascotInfile.html#abf43eb688305547427be2a7151dd89d0">  217</a></span>&#160;    <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1MascotInfile.html#abf43eb688305547427be2a7151dd89d0">search_type_</a>;</div>
<div class="line"><a name="l00218"></a><span class="lineno">  218</span>&#160;</div>
<div class="line"><a name="l00220"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MascotInfile.html#a86d2838e4d657997d23b7fedc4a0de70">  220</a></span>&#160;    <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1MascotInfile.html#a86d2838e4d657997d23b7fedc4a0de70">hits_</a>;</div>
<div class="line"><a name="l00221"></a><span class="lineno">  221</span>&#160;</div>
<div class="line"><a name="l00223"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MascotInfile.html#a7673e018c0978798abbc46a8cae0d1b0">  223</a></span>&#160;    <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1MascotInfile.html#a7673e018c0978798abbc46a8cae0d1b0">cleavage_</a>;</div>
<div class="line"><a name="l00224"></a><span class="lineno">  224</span>&#160;</div>
<div class="line"><a name="l00226"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MascotInfile.html#a560f7947ffcdcda57633e2766a14bf3c">  226</a></span>&#160;    <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1MascotInfile.html#a560f7947ffcdcda57633e2766a14bf3c">mass_type_</a>;</div>
<div class="line"><a name="l00227"></a><span class="lineno">  227</span>&#160;</div>
<div class="line"><a name="l00229"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MascotInfile.html#a05b93b555b7cb9a301af33a341b02c2e">  229</a></span>&#160;    std::vector&lt;String&gt; <a class="code" href="classOpenMS_1_1MascotInfile.html#a05b93b555b7cb9a301af33a341b02c2e">mods_</a>;</div>
<div class="line"><a name="l00230"></a><span class="lineno">  230</span>&#160;</div>
<div class="line"><a name="l00232"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MascotInfile.html#aa512ee85172fb565d820fad1e74cd4d2">  232</a></span>&#160;    std::vector&lt;String&gt; <a class="code" href="classOpenMS_1_1MascotInfile.html#aa512ee85172fb565d820fad1e74cd4d2">variable_mods_</a>;</div>
<div class="line"><a name="l00233"></a><span class="lineno">  233</span>&#160;</div>
<div class="line"><a name="l00235"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MascotInfile.html#a0a98f2bc76af916a1e5030127497808c">  235</a></span>&#160;    <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1MascotInfile.html#a0a98f2bc76af916a1e5030127497808c">instrument_</a>;</div>
<div class="line"><a name="l00236"></a><span class="lineno">  236</span>&#160;</div>
<div class="line"><a name="l00238"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MascotInfile.html#a783b61967acca152646ef96765ca1c3e">  238</a></span>&#160;    <a class="code" href="classunsigned_01int.html">UInt</a> <a class="code" href="classOpenMS_1_1MascotInfile.html#a783b61967acca152646ef96765ca1c3e">missed_cleavages_</a>;</div>
<div class="line"><a name="l00239"></a><span class="lineno">  239</span>&#160;</div>
<div class="line"><a name="l00241"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MascotInfile.html#a17921ca118ae3d8d972b748147f5ef6b">  241</a></span>&#160;    <a class="code" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a> <a class="code" href="classOpenMS_1_1MascotInfile.html#a17921ca118ae3d8d972b748147f5ef6b">precursor_mass_tolerance_</a>;</div>
<div class="line"><a name="l00242"></a><span class="lineno">  242</span>&#160;</div>
<div class="line"><a name="l00244"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MascotInfile.html#a0a90201eb5e89b7edbb822b3c5bf7e05">  244</a></span>&#160;    <a class="code" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a> <a class="code" href="classOpenMS_1_1MascotInfile.html#a0a90201eb5e89b7edbb822b3c5bf7e05">ion_mass_tolerance_</a>;</div>
<div class="line"><a name="l00245"></a><span class="lineno">  245</span>&#160;</div>
<div class="line"><a name="l00247"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MascotInfile.html#a1bcd6b859be00c67e8276dd446e8200d">  247</a></span>&#160;    <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1MascotInfile.html#a1bcd6b859be00c67e8276dd446e8200d">taxonomy_</a>;</div>
<div class="line"><a name="l00248"></a><span class="lineno">  248</span>&#160;</div>
<div class="line"><a name="l00250"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MascotInfile.html#a407082e00e9ef69130127de8dd3431b9">  250</a></span>&#160;    <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1MascotInfile.html#a407082e00e9ef69130127de8dd3431b9">form_version_</a>;</div>
<div class="line"><a name="l00251"></a><span class="lineno">  251</span>&#160;</div>
<div class="line"><a name="l00253"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MascotInfile.html#a49cc1f20edc5ca4fdef5b0ecdde80d78">  253</a></span>&#160;    <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1MascotInfile.html#a49cc1f20edc5ca4fdef5b0ecdde80d78">boundary_</a>;</div>
<div class="line"><a name="l00254"></a><span class="lineno">  254</span>&#160;</div>
<div class="line"><a name="l00256"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MascotInfile.html#af4eca834d1d6d03252647c8261d43bfe">  256</a></span>&#160;    <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1MascotInfile.html#af4eca834d1d6d03252647c8261d43bfe">retention_time_</a>;</div>
<div class="line"><a name="l00257"></a><span class="lineno">  257</span>&#160;</div>
<div class="line"><a name="l00259"></a><span class="lineno">  259</span>&#160;    <span class="keywordtype">void</span> writeParameterHeader_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; name, FILE * fp, <span class="keywordtype">bool</span> line_break = <span class="keyword">true</span>);</div>
<div class="line"><a name="l00260"></a><span class="lineno">  260</span>&#160;</div>
<div class="line"><a name="l00262"></a><span class="lineno">  262</span>&#160;    <span class="keywordtype">void</span> writeHeader_(FILE * fp);</div>
<div class="line"><a name="l00263"></a><span class="lineno">  263</span>&#160;</div>
<div class="line"><a name="l00265"></a><span class="lineno">  265</span>&#160;    <span class="keywordtype">void</span> writeSpectrum_(FILE * fp,</div>
<div class="line"><a name="l00266"></a><span class="lineno">  266</span>&#160;                        <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; filename,</div>
<div class="line"><a name="l00267"></a><span class="lineno">  267</span>&#160;                        <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html">PeakSpectrum</a> &amp; peaks);</div>
<div class="line"><a name="l00268"></a><span class="lineno">  268</span>&#160;</div>
<div class="line"><a name="l00270"></a><span class="lineno">  270</span>&#160;    <span class="keywordtype">void</span> writeMSExperiment_(FILE * fp,</div>
<div class="line"><a name="l00271"></a><span class="lineno">  271</span>&#160;                            <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; filename,</div>
<div class="line"><a name="l00272"></a><span class="lineno">  272</span>&#160;                            <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment&lt;&gt;</a> &amp; experiment);</div>
<div class="line"><a name="l00273"></a><span class="lineno">  273</span>&#160;</div>
<div class="line"><a name="l00274"></a><span class="lineno">  274</span>&#160;    <span class="keywordtype">bool</span> getNextSpectrum_(std::istream &amp; is, std::vector&lt;std::pair&lt;double, double&gt; &gt; &amp; spectrum, <a class="code" href="classunsigned_01int.html">UInt</a> &amp; charge, <span class="keywordtype">double</span> &amp; precursor_mz, <span class="keywordtype">double</span> &amp; precursor_int, <span class="keywordtype">double</span> &amp; rt, <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; title);</div>
<div class="line"><a name="l00275"></a><span class="lineno">  275</span>&#160;  };</div>
<div class="line"><a name="l00276"></a><span class="lineno">  276</span>&#160;</div>
<div class="line"><a name="l00277"></a><span class="lineno">  277</span>&#160;} <span class="comment">// namespace OpenMS</span></div>
<div class="line"><a name="l00278"></a><span class="lineno">  278</span>&#160;</div>
<div class="line"><a name="l00279"></a><span class="lineno">  279</span>&#160;<span class="preprocessor">#endif // OPENMS_FORMAT_MASCOTINFILE_H</span></div>
<div class="ttc" id="classunsigned_01int_html"><div class="ttname"><a href="classunsigned_01int.html">unsigned int</a></div></div>
<div class="ttc" id="StandardTypes_8h_html"><div class="ttname"><a href="StandardTypes_8h.html">StandardTypes.h</a></div></div>
<div class="ttc" id="group__Concept_html_gab685845059e8a2c92743427d9a698c70"><div class="ttname"><a href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">OpenMS::Real</a></div><div class="ttdeci">float Real</div><div class="ttdoc">Real type. </div><div class="ttdef"><b>Definition:</b> Types.h:109</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_1MascotInfile_html_a41ab11ce76df5f4c9eb364c63d7e6eba"><div class="ttname"><a href="classOpenMS_1_1MascotInfile.html#a41ab11ce76df5f4c9eb364c63d7e6eba">OpenMS::MascotInfile::search_title_</a></div><div class="ttdeci">String search_title_</div><div class="ttdoc">the search title of the mascot search </div><div class="ttdef"><b>Definition:</b> MascotInfile.h:211</div></div>
<div class="ttc" id="classOpenMS_1_1MascotInfile_html_af4eca834d1d6d03252647c8261d43bfe"><div class="ttname"><a href="classOpenMS_1_1MascotInfile.html#af4eca834d1d6d03252647c8261d43bfe">OpenMS::MascotInfile::retention_time_</a></div><div class="ttdeci">DoubleReal retention_time_</div><div class="ttdoc">the retention time </div><div class="ttdef"><b>Definition:</b> MascotInfile.h:256</div></div>
<div class="ttc" id="classOpenMS_1_1MascotInfile_html_a98bebe67b8b06a9a67a3654d631355b4"><div class="ttname"><a href="classOpenMS_1_1MascotInfile.html#a98bebe67b8b06a9a67a3654d631355b4">OpenMS::MascotInfile::load</a></div><div class="ttdeci">void load(const String &amp;filename, MapType &amp;exp)</div><div class="ttdef"><b>Definition:</b> MascotInfile.h:83</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_1MascotInfile_html_a560f7947ffcdcda57633e2766a14bf3c"><div class="ttname"><a href="classOpenMS_1_1MascotInfile.html#a560f7947ffcdcda57633e2766a14bf3c">OpenMS::MascotInfile::mass_type_</a></div><div class="ttdeci">String mass_type_</div><div class="ttdoc">Monoisotopic/average mass. </div><div class="ttdef"><b>Definition:</b> MascotInfile.h:226</div></div>
<div class="ttc" id="namespaceOpenMS_html_a013338b7bdbb5c3b4c78666656070e23"><div class="ttname"><a href="namespaceOpenMS.html#a013338b7bdbb5c3b4c78666656070e23">OpenMS::PeakType</a></div><div class="ttdeci">Peak2D PeakType</div><div class="ttdef"><b>Definition:</b> MassTrace.h:49</div></div>
<div class="ttc" id="classdouble_html"><div class="ttname"><a href="classdouble.html">double</a></div></div>
<div class="ttc" id="classOpenMS_1_1MascotInfile_html_a783b61967acca152646ef96765ca1c3e"><div class="ttname"><a href="classOpenMS_1_1MascotInfile.html#a783b61967acca152646ef96765ca1c3e">OpenMS::MascotInfile::missed_cleavages_</a></div><div class="ttdeci">UInt missed_cleavages_</div><div class="ttdoc">number of missed cleavages </div><div class="ttdef"><b>Definition:</b> MascotInfile.h:238</div></div>
<div class="ttc" id="classOpenMS_1_1MascotInfile_html_a0a90201eb5e89b7edbb822b3c5bf7e05"><div class="ttname"><a href="classOpenMS_1_1MascotInfile.html#a0a90201eb5e89b7edbb822b3c5bf7e05">OpenMS::MascotInfile::ion_mass_tolerance_</a></div><div class="ttdeci">Real ion_mass_tolerance_</div><div class="ttdoc">m/z tolerance of ions in Da </div><div class="ttdef"><b>Definition:</b> MascotInfile.h:244</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_1MascotInfile_html_afc5f9aaffcc298be4bd38a79480ed304"><div class="ttname"><a href="classOpenMS_1_1MascotInfile.html#afc5f9aaffcc298be4bd38a79480ed304">OpenMS::MascotInfile::charges_</a></div><div class="ttdeci">String charges_</div><div class="ttdoc">charge states to use </div><div class="ttdef"><b>Definition:</b> MascotInfile.h:208</div></div>
<div class="ttc" id="classOpenMS_1_1MascotInfile_html_a1bcd6b859be00c67e8276dd446e8200d"><div class="ttname"><a href="classOpenMS_1_1MascotInfile.html#a1bcd6b859be00c67e8276dd446e8200d">OpenMS::MascotInfile::taxonomy_</a></div><div class="ttdeci">String taxonomy_</div><div class="ttdoc">taxonomy </div><div class="ttdef"><b>Definition:</b> MascotInfile.h:247</div></div>
<div class="ttc" id="File_8h_html"><div class="ttname"><a href="File_8h.html">File.h</a></div></div>
<div class="ttc" id="MSExperiment_8h_html"><div class="ttname"><a href="MSExperiment_8h.html">MSExperiment.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1MSSpectrum_html"><div class="ttname"><a href="classOpenMS_1_1MSSpectrum.html">OpenMS::MSSpectrum&lt; Peak1D &gt;</a></div></div>
<div class="ttc" id="classOpenMS_1_1File_html_a103bc592f26fed81f56f2f92b7ab5063"><div class="ttname"><a href="classOpenMS_1_1File.html#a103bc592f26fed81f56f2f92b7ab5063">OpenMS::File::exists</a></div><div class="ttdeci">static bool exists(const String &amp;file)</div><div class="ttdoc">Method used to test if a file exists. </div></div>
<div class="ttc" id="classOpenMS_1_1MascotInfile_html_a488bf544f6efc29a3265943c28aba0f2"><div class="ttname"><a href="classOpenMS_1_1MascotInfile.html#a488bf544f6efc29a3265943c28aba0f2">OpenMS::MascotInfile::db_</a></div><div class="ttdeci">String db_</div><div class="ttdoc">the DB to search in </div><div class="ttdef"><b>Definition:</b> MascotInfile.h:214</div></div>
<div class="ttc" id="classOpenMS_1_1MascotInfile_html_a0a98f2bc76af916a1e5030127497808c"><div class="ttname"><a href="classOpenMS_1_1MascotInfile.html#a0a98f2bc76af916a1e5030127497808c">OpenMS::MascotInfile::instrument_</a></div><div class="ttdeci">String instrument_</div><div class="ttdoc">the used instument </div><div class="ttdef"><b>Definition:</b> MascotInfile.h:235</div></div>
<div class="ttc" id="classOpenMS_1_1Peak2D_html_abbdecccbbcf763c6c5eae3b7c3cb915e"><div class="ttname"><a href="classOpenMS_1_1Peak2D.html#abbdecccbbcf763c6c5eae3b7c3cb915e">OpenMS::Peak2D::setPosition</a></div><div class="ttdeci">void setPosition(const PositionType &amp;position)</div><div class="ttdoc">Mutable access to the position. </div><div class="ttdef"><b>Definition:</b> Peak2D.h:185</div></div>
<div class="ttc" id="classOpenMS_1_1MascotInfile_html_ae23f3c856a76faaa8a37015bd7fef8bc"><div class="ttname"><a href="classOpenMS_1_1MascotInfile.html#ae23f3c856a76faaa8a37015bd7fef8bc">OpenMS::MascotInfile::mz_</a></div><div class="ttdeci">DoubleReal mz_</div><div class="ttdoc">parent mass </div><div class="ttdef"><b>Definition:</b> MascotInfile.h:205</div></div>
<div class="ttc" id="classOpenMS_1_1MascotInfile_html_a17921ca118ae3d8d972b748147f5ef6b"><div class="ttname"><a href="classOpenMS_1_1MascotInfile.html#a17921ca118ae3d8d972b748147f5ef6b">OpenMS::MascotInfile::precursor_mass_tolerance_</a></div><div class="ttdeci">Real precursor_mass_tolerance_</div><div class="ttdoc">precursor mass toerance in Da </div><div class="ttdef"><b>Definition:</b> MascotInfile.h:241</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_1MascotInfile_html_a407082e00e9ef69130127de8dd3431b9"><div class="ttname"><a href="classOpenMS_1_1MascotInfile.html#a407082e00e9ef69130127de8dd3431b9">OpenMS::MascotInfile::form_version_</a></div><div class="ttdeci">String form_version_</div><div class="ttdoc">form version </div><div class="ttdef"><b>Definition:</b> MascotInfile.h:250</div></div>
<div class="ttc" id="classOpenMS_1_1MascotInfile_html_aa512ee85172fb565d820fad1e74cd4d2"><div class="ttname"><a href="classOpenMS_1_1MascotInfile.html#aa512ee85172fb565d820fad1e74cd4d2">OpenMS::MascotInfile::variable_mods_</a></div><div class="ttdeci">std::vector&lt; String &gt; variable_mods_</div><div class="ttdoc">variable Modifications </div><div class="ttdef"><b>Definition:</b> MascotInfile.h:232</div></div>
<div class="ttc" id="classOpenMS_1_1MascotInfile_html_a05b93b555b7cb9a301af33a341b02c2e"><div class="ttname"><a href="classOpenMS_1_1MascotInfile.html#a05b93b555b7cb9a301af33a341b02c2e">OpenMS::MascotInfile::mods_</a></div><div class="ttdeci">std::vector&lt; String &gt; mods_</div><div class="ttdoc">fixed Modifications </div><div class="ttdef"><b>Definition:</b> MascotInfile.h:229</div></div>
<div class="ttc" id="classOpenMS_1_1MascotInfile_html_abf43eb688305547427be2a7151dd89d0"><div class="ttname"><a href="classOpenMS_1_1MascotInfile.html#abf43eb688305547427be2a7151dd89d0">OpenMS::MascotInfile::search_type_</a></div><div class="ttdeci">String search_type_</div><div class="ttdoc">search type: MIS, SQ or PMF </div><div class="ttdef"><b>Definition:</b> MascotInfile.h:217</div></div>
<div class="ttc" id="classOpenMS_1_1MascotInfile_html"><div class="ttname"><a href="classOpenMS_1_1MascotInfile.html">OpenMS::MascotInfile</a></div><div class="ttdoc">Mascot input file adapter. </div><div class="ttdef"><b>Definition:</b> MascotInfile.h:59</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_1MascotInfile_html_a7673e018c0978798abbc46a8cae0d1b0"><div class="ttname"><a href="classOpenMS_1_1MascotInfile.html#a7673e018c0978798abbc46a8cae0d1b0">OpenMS::MascotInfile::cleavage_</a></div><div class="ttdeci">String cleavage_</div><div class="ttdoc">Enzyme used for cleavage. </div><div class="ttdef"><b>Definition:</b> MascotInfile.h:223</div></div>
<div class="ttc" id="classOpenMS_1_1MascotInfile_html_a86d2838e4d657997d23b7fedc4a0de70"><div class="ttname"><a href="classOpenMS_1_1MascotInfile.html#a86d2838e4d657997d23b7fedc4a0de70">OpenMS::MascotInfile::hits_</a></div><div class="ttdeci">String hits_</div><div class="ttdoc">number of hits to report </div><div class="ttdef"><b>Definition:</b> MascotInfile.h:220</div></div>
<div class="ttc" id="String_8h_html"><div class="ttname"><a href="String_8h.html">String.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1MascotInfile_html_a49cc1f20edc5ca4fdef5b0ecdde80d78"><div class="ttname"><a href="classOpenMS_1_1MascotInfile.html#a49cc1f20edc5ca4fdef5b0ecdde80d78">OpenMS::MascotInfile::boundary_</a></div><div class="ttdeci">String boundary_</div><div class="ttdoc">the boundary used for the MIME format </div><div class="ttdef"><b>Definition:</b> MascotInfile.h:253</div></div>
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<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
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