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<div class="title">IMSAlphabetParser.h</div> </div>
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<a href="IMSAlphabetParser_8h.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="comment">// OpenMS -- Open-Source Mass Spectrometry</span></div>
<div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="comment">// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,</span></div>
<div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="comment">// ETH Zurich, and Freie Universitaet Berlin 2002-2013.</span></div>
<div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="comment">//</span></div>
<div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="comment">// This software is released under a three-clause BSD license:</span></div>
<div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="comment">// * Redistributions of source code must retain the above copyright</span></div>
<div class="line"><a name="l00009"></a><span class="lineno"> 9</span> <span class="comment">// notice, this list of conditions and the following disclaimer.</span></div>
<div class="line"><a name="l00010"></a><span class="lineno"> 10</span> <span class="comment">// * Redistributions in binary form must reproduce the above copyright</span></div>
<div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="comment">// notice, this list of conditions and the following disclaimer in the</span></div>
<div class="line"><a name="l00012"></a><span class="lineno"> 12</span> <span class="comment">// documentation and/or other materials provided with the distribution.</span></div>
<div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="comment">// * Neither the name of any author or any participating institution</span></div>
<div class="line"><a name="l00014"></a><span class="lineno"> 14</span> <span class="comment">// may be used to endorse or promote products derived from this software</span></div>
<div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="comment">// without specific prior written permission.</span></div>
<div class="line"><a name="l00016"></a><span class="lineno"> 16</span> <span class="comment">// For a full list of authors, refer to the file AUTHORS.</span></div>
<div class="line"><a name="l00017"></a><span class="lineno"> 17</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00018"></a><span class="lineno"> 18</span> <span class="comment">// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"</span></div>
<div class="line"><a name="l00019"></a><span class="lineno"> 19</span> <span class="comment">// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE</span></div>
<div class="line"><a name="l00020"></a><span class="lineno"> 20</span> <span class="comment">// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE</span></div>
<div class="line"><a name="l00021"></a><span class="lineno"> 21</span> <span class="comment">// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING</span></div>
<div class="line"><a name="l00022"></a><span class="lineno"> 22</span> <span class="comment">// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,</span></div>
<div class="line"><a name="l00023"></a><span class="lineno"> 23</span> <span class="comment">// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,</span></div>
<div class="line"><a name="l00024"></a><span class="lineno"> 24</span> <span class="comment">// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;</span></div>
<div class="line"><a name="l00025"></a><span class="lineno"> 25</span> <span class="comment">// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,</span></div>
<div class="line"><a name="l00026"></a><span class="lineno"> 26</span> <span class="comment">// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR</span></div>
<div class="line"><a name="l00027"></a><span class="lineno"> 27</span> <span class="comment">// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF</span></div>
<div class="line"><a name="l00028"></a><span class="lineno"> 28</span> <span class="comment">// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</span></div>
<div class="line"><a name="l00029"></a><span class="lineno"> 29</span> <span class="comment">//</span></div>
<div class="line"><a name="l00030"></a><span class="lineno"> 30</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00031"></a><span class="lineno"> 31</span> <span class="comment">// $Maintainer: Stephan Aiche $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno"> 32</span> <span class="comment">// $Authors: Anton Pervukhin <Anton.Pervukhin@CeBiTec.Uni-Bielefeld.DE> $</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> <span class="comment">//</span></div>
<div class="line"><a name="l00035"></a><span class="lineno"> 35</span> </div>
<div class="line"><a name="l00036"></a><span class="lineno"> 36</span> <span class="preprocessor">#ifndef OPENMS_CHEMISTRY_MASSDECOMPOSITION_IMS_IMSALPHABETPARSER_H</span></div>
<div class="line"><a name="l00037"></a><span class="lineno"> 37</span> <span class="preprocessor"></span><span class="preprocessor">#define OPENMS_CHEMISTRY_MASSDECOMPOSITION_IMS_IMSALPHABETPARSER_H</span></div>
<div class="line"><a name="l00038"></a><span class="lineno"> 38</span> <span class="preprocessor"></span></div>
<div class="line"><a name="l00039"></a><span class="lineno"> 39</span> <span class="preprocessor">#include <fstream></span></div>
<div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="preprocessor">#include <istream></span></div>
<div class="line"><a name="l00041"></a><span class="lineno"> 41</span> <span class="preprocessor">#include <map></span></div>
<div class="line"><a name="l00042"></a><span class="lineno"> 42</span> <span class="preprocessor">#include <string></span></div>
<div class="line"><a name="l00043"></a><span class="lineno"> 43</span> </div>
<div class="line"><a name="l00044"></a><span class="lineno"> 44</span> <span class="preprocessor">#include <<a class="code" href="Exception_8h.html">OpenMS/CONCEPT/Exception.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="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00047"></a><span class="lineno"> 47</span> {</div>
<div class="line"><a name="l00048"></a><span class="lineno"> 48</span> </div>
<div class="line"><a name="l00049"></a><span class="lineno"> 49</span>  <span class="keyword">namespace </span>ims</div>
<div class="line"><a name="l00050"></a><span class="lineno"> 50</span>  {</div>
<div class="line"><a name="l00051"></a><span class="lineno"> 51</span> </div>
<div class="line"><a name="l00061"></a><span class="lineno"> 61</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> AlphabetElementType = <a class="code" href="classdouble.html">double</a>,</div>
<div class="line"><a name="l00062"></a><span class="lineno"> 62</span>  <span class="keyword">typename</span> Container = std::map<std::string, AlphabetElementType>,</div>
<div class="line"><a name="l00063"></a><span class="lineno"> 63</span>  <span class="keyword">typename</span> InputSource = std::istream></div>
<div class="line"><a name="l00064"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ims_1_1IMSAlphabetParser.html"> 64</a></span>  <span class="keyword">class </span><a class="code" href="classOpenMS_1_1ims_1_1IMSAlphabetParser.html">IMSAlphabetParser</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="l00070"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ims_1_1IMSAlphabetParser.html#ab6acf6aaa4bab8b5a1349a7318aa9ad4"> 70</a></span>  <span class="keyword">typedef</span> Container <a class="code" href="classOpenMS_1_1ims_1_1IMSAlphabetParser.html#ab6acf6aaa4bab8b5a1349a7318aa9ad4">ContainerType</a>;</div>
<div class="line"><a name="l00071"></a><span class="lineno"> 71</span> </div>
<div class="line"><a name="l00079"></a><span class="lineno"> 79</span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1ims_1_1IMSAlphabetParser.html#ae242eda4bd468cf17a0d503f13add026">load</a>(<span class="keyword">const</span> std::string & fname);</div>
<div class="line"><a name="l00080"></a><span class="lineno"> 80</span> </div>
<div class="line"><a name="l00086"></a><span class="lineno"> 86</span>  <span class="keyword">virtual</span> <a class="code" href="classOpenMS_1_1ims_1_1IMSAlphabetParser.html#ab6acf6aaa4bab8b5a1349a7318aa9ad4">ContainerType</a> & <a class="code" href="classOpenMS_1_1ims_1_1IMSAlphabetParser.html#a1df0ceed98c6c369158f1761effb7035">getElements</a>() = 0;</div>
<div class="line"><a name="l00087"></a><span class="lineno"> 87</span> </div>
<div class="line"><a name="l00093"></a><span class="lineno"> 93</span>  <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1ims_1_1IMSAlphabetParser.html#ade573b26af8953d802a34ed40aef4e7d">parse</a>(InputSource & is) = 0;</div>
<div class="line"><a name="l00094"></a><span class="lineno"> 94</span> </div>
<div class="line"><a name="l00096"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ims_1_1IMSAlphabetParser.html#a9f3c7268f0ee25dff8c0703da0e58f8e"> 96</a></span>  <span class="keyword">virtual</span> <a class="code" href="classOpenMS_1_1ims_1_1IMSAlphabetParser.html#a9f3c7268f0ee25dff8c0703da0e58f8e">~IMSAlphabetParser</a>() {}</div>
<div class="line"><a name="l00097"></a><span class="lineno"> 97</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>  <span class="keyword">template</span> <<span class="keyword">typename</span> AlphabetElementType, <span class="keyword">typename</span> Container, <span class="keyword">typename</span> InputSource></div>
<div class="line"><a name="l00100"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ims_1_1IMSAlphabetParser.html#ae242eda4bd468cf17a0d503f13add026"> 100</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1ims_1_1IMSAlphabetParser.html#ae242eda4bd468cf17a0d503f13add026">IMSAlphabetParser<AlphabetElementType, Container, InputSource>::load</a>(<span class="keyword">const</span> std::string & fname)</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>  std::ifstream ifs(fname.c_str());</div>
<div class="line"><a name="l00103"></a><span class="lineno"> 103</span>  <span class="keywordflow">if</span> (!ifs)</div>
<div class="line"><a name="l00104"></a><span class="lineno"> 104</span>  {</div>
<div class="line"><a name="l00105"></a><span class="lineno"> 105</span>  <span class="keywordflow">throw</span> <a class="code" href="classOpenMS_1_1Exception_1_1IOException.html">Exception::IOException</a>(__FILE__, __LINE__, __PRETTY_FUNCTION__, fname);</div>
<div class="line"><a name="l00106"></a><span class="lineno"> 106</span>  }</div>
<div class="line"><a name="l00107"></a><span class="lineno"> 107</span>  this->parse(ifs);</div>
<div class="line"><a name="l00108"></a><span class="lineno"> 108</span>  }</div>
<div class="line"><a name="l00109"></a><span class="lineno"> 109</span> </div>
<div class="line"><a name="l00110"></a><span class="lineno"> 110</span>  } <span class="comment">// namespace ims</span></div>
<div class="line"><a name="l00111"></a><span class="lineno"> 111</span> } <span class="comment">// namespace OpenMS</span></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> <span class="preprocessor">#endif // OPENMS_CHEMISTRY_MASSDECOMPOSITION_IMS_ALPHABETPARSER_H</span></div>
<div class="ttc" id="classOpenMS_1_1ims_1_1IMSAlphabetParser_html_a1df0ceed98c6c369158f1761effb7035"><div class="ttname"><a href="classOpenMS_1_1ims_1_1IMSAlphabetParser.html#a1df0ceed98c6c369158f1761effb7035">OpenMS::ims::IMSAlphabetParser::getElements</a></div><div class="ttdeci">virtual ContainerType & getElements()=0</div></div>
<div class="ttc" id="classOpenMS_1_1ims_1_1IMSAlphabetParser_html_ade573b26af8953d802a34ed40aef4e7d"><div class="ttname"><a href="classOpenMS_1_1ims_1_1IMSAlphabetParser.html#ade573b26af8953d802a34ed40aef4e7d">OpenMS::ims::IMSAlphabetParser::parse</a></div><div class="ttdeci">virtual void parse(InputSource &is)=0</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_1ims_1_1IMSAlphabetParser_html_ae242eda4bd468cf17a0d503f13add026"><div class="ttname"><a href="classOpenMS_1_1ims_1_1IMSAlphabetParser.html#ae242eda4bd468cf17a0d503f13add026">OpenMS::ims::IMSAlphabetParser::load</a></div><div class="ttdeci">void load(const std::string &fname)</div><div class="ttdef"><b>Definition:</b> IMSAlphabetParser.h:100</div></div>
<div class="ttc" id="classOpenMS_1_1ims_1_1IMSAlphabetParser_html_ab6acf6aaa4bab8b5a1349a7318aa9ad4"><div class="ttname"><a href="classOpenMS_1_1ims_1_1IMSAlphabetParser.html#ab6acf6aaa4bab8b5a1349a7318aa9ad4">OpenMS::ims::IMSAlphabetParser::ContainerType</a></div><div class="ttdeci">Container ContainerType</div><div class="ttdef"><b>Definition:</b> IMSAlphabetParser.h:70</div></div>
<div class="ttc" id="classOpenMS_1_1ims_1_1IMSAlphabetParser_html_a9f3c7268f0ee25dff8c0703da0e58f8e"><div class="ttname"><a href="classOpenMS_1_1ims_1_1IMSAlphabetParser.html#a9f3c7268f0ee25dff8c0703da0e58f8e">OpenMS::ims::IMSAlphabetParser::~IMSAlphabetParser</a></div><div class="ttdeci">virtual ~IMSAlphabetParser()</div><div class="ttdoc">Destructor. </div><div class="ttdef"><b>Definition:</b> IMSAlphabetParser.h:96</div></div>
<div class="ttc" id="classOpenMS_1_1Exception_1_1IOException_html"><div class="ttname"><a href="classOpenMS_1_1Exception_1_1IOException.html">OpenMS::Exception::IOException</a></div><div class="ttdoc">General IOException. </div><div class="ttdef"><b>Definition:</b> Exception.h:566</div></div>
<div class="ttc" id="classOpenMS_1_1ims_1_1IMSAlphabetParser_html"><div class="ttname"><a href="classOpenMS_1_1ims_1_1IMSAlphabetParser.html">OpenMS::ims::IMSAlphabetParser</a></div><div class="ttdoc">An abstract templatized parser to load the data that is used to initialize Alphabet objects...</div><div class="ttdef"><b>Definition:</b> IMSAlphabetParser.h:64</div></div>
<div class="ttc" id="Exception_8h_html"><div class="ttname"><a href="Exception_8h.html">Exception.h</a></div></div>
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