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<a href="SpecArrayFile_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>
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<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: Chris Bielow $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160;<span class="comment">// $Authors: Chris Bielow $</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_SPECARRAYFILE_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_SPECARRAYFILE_H</span></div>
<div class="line"><a name="l00037"></a><span class="lineno">   37</span>&#160;<span class="preprocessor"></span></div>
<div class="line"><a name="l00038"></a><span class="lineno">   38</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="String_8h.html">OpenMS/DATASTRUCTURES/String.h</a>&gt;</span></div>
<div class="line"><a name="l00039"></a><span class="lineno">   39</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="Exception_8h.html">OpenMS/CONCEPT/Exception.h</a>&gt;</span></div>
<div class="line"><a name="l00040"></a><span class="lineno">   40</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="LogStream_8h.html">OpenMS/CONCEPT/LogStream.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="Feature_8h.html">OpenMS/KERNEL/Feature.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="TextFile_8h.html">OpenMS/FORMAT/TextFile.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;fstream&gt;</span></div>
<div class="line"><a name="l00045"></a><span class="lineno">   45</span>&#160;<span class="preprocessor">#include &lt;vector&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="l00061"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SpecArrayFile.html">   61</a></span>&#160;  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1SpecArrayFile.html">SpecArrayFile</a></div>
<div class="line"><a name="l00062"></a><span class="lineno">   62</span>&#160;  {</div>
<div class="line"><a name="l00063"></a><span class="lineno">   63</span>&#160;<span class="keyword">public</span>:</div>
<div class="line"><a name="l00065"></a><span class="lineno">   65</span>&#160;    <a class="code" href="classOpenMS_1_1SpecArrayFile.html">SpecArrayFile</a>();</div>
<div class="line"><a name="l00067"></a><span class="lineno">   67</span>&#160;    <span class="keyword">virtual</span> ~<a class="code" href="classOpenMS_1_1SpecArrayFile.html">SpecArrayFile</a>();</div>
<div class="line"><a name="l00068"></a><span class="lineno">   68</span>&#160;</div>
<div class="line"><a name="l00077"></a><span class="lineno">   77</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">typename</span> FeatureMapType&gt;</div>
<div class="line"><a name="l00078"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SpecArrayFile.html#aa4e73ca60efa3ca29e203f46b5187c6c">   78</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1SpecArrayFile.html#aa4e73ca60efa3ca29e203f46b5187c6c">load</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; filename, FeatureMapType &amp; feature_map)</div>
<div class="line"><a name="l00079"></a><span class="lineno">   79</span>&#160;    {</div>
<div class="line"><a name="l00080"></a><span class="lineno">   80</span>&#160;      <span class="comment">// load input</span></div>
<div class="line"><a name="l00081"></a><span class="lineno">   81</span>&#160;      <a class="code" href="classOpenMS_1_1TextFile.html">TextFile</a> input(filename, <span class="keyword">false</span>);</div>
<div class="line"><a name="l00082"></a><span class="lineno">   82</span>&#160;</div>
<div class="line"><a name="l00083"></a><span class="lineno">   83</span>&#160;      <span class="comment">// reset map</span></div>
<div class="line"><a name="l00084"></a><span class="lineno">   84</span>&#160;      FeatureMapType fmap;</div>
<div class="line"><a name="l00085"></a><span class="lineno">   85</span>&#160;      feature_map = fmap;</div>
<div class="line"><a name="l00086"></a><span class="lineno">   86</span>&#160;</div>
<div class="line"><a name="l00087"></a><span class="lineno">   87</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 1; i &lt; input.size(); ++i)</div>
<div class="line"><a name="l00088"></a><span class="lineno">   88</span>&#160;      {</div>
<div class="line"><a name="l00089"></a><span class="lineno">   89</span>&#160;        <a class="code" href="classOpenMS_1_1String.html">String</a> line = input[i];</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::vector&lt;String&gt; parts;</div>
<div class="line"><a name="l00092"></a><span class="lineno">   92</span>&#160;        line.<a class="code" href="classOpenMS_1_1String.html#ae580d960e12c7f0ebc5c95931cf39ad5">split</a>(<span class="charliteral">&#39;\t&#39;</span>, parts);</div>
<div class="line"><a name="l00093"></a><span class="lineno">   93</span>&#160;</div>
<div class="line"><a name="l00094"></a><span class="lineno">   94</span>&#160;        <span class="keywordflow">if</span> (parts.size() &lt; 5)</div>
<div class="line"><a name="l00095"></a><span class="lineno">   95</span>&#160;        {</div>
<div class="line"><a name="l00096"></a><span class="lineno">   96</span>&#160;          <span class="keywordflow">throw</span> <a class="code" href="classOpenMS_1_1Exception_1_1ParseError.html">Exception::ParseError</a>(__FILE__, __LINE__, __PRETTY_FUNCTION__, <span class="stringliteral">&quot;&quot;</span>, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;Failed to convert line&quot;</span>)  + <a class="code" href="classOpenMS_1_1String.html">String</a>(i + 1) + <span class="stringliteral">&quot;not enough columns (expected 5 or more, got &quot;</span> + <a class="code" href="classOpenMS_1_1String.html">String</a>(parts.size()) + <span class="stringliteral">&quot;)&quot;</span>);</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;</div>
<div class="line"><a name="l00099"></a><span class="lineno">   99</span>&#160;        <a class="code" href="classOpenMS_1_1Feature.html">Feature</a> f;</div>
<div class="line"><a name="l00100"></a><span class="lineno">  100</span>&#160;        <span class="keywordflow">try</span></div>
<div class="line"><a name="l00101"></a><span class="lineno">  101</span>&#160;        {</div>
<div class="line"><a name="l00102"></a><span class="lineno">  102</span>&#160;          f.<a class="code" href="classOpenMS_1_1Peak2D.html#a2694f0775c46d9076355cb85d9815425">setMZ</a>(parts[0].toDouble());</div>
<div class="line"><a name="l00103"></a><span class="lineno">  103</span>&#160;          f.<a class="code" href="classOpenMS_1_1Peak2D.html#a396c5ebcac2e70f9b9a478bb2456985b">setRT</a>(parts[1].toDouble() * 60.0);</div>
<div class="line"><a name="l00104"></a><span class="lineno">  104</span>&#160;          f.<a class="code" href="classOpenMS_1_1MetaInfoInterface.html#a135a7e818125b31198a8a65d9ac7a3d1">setMetaValue</a>(<span class="stringliteral">&quot;s/n&quot;</span>, parts[2].toDouble());</div>
<div class="line"><a name="l00105"></a><span class="lineno">  105</span>&#160;          f.<a class="code" href="classOpenMS_1_1BaseFeature.html#ab595724fe9b9eb5d37011f07d90b9e0b">setCharge</a>(parts[3].toInt());</div>
<div class="line"><a name="l00106"></a><span class="lineno">  106</span>&#160;          f.<a class="code" href="classOpenMS_1_1Peak2D.html#ab875c2479c6cd2a0189e4684bfa4f97d">setIntensity</a>(parts[4].toDouble());</div>
<div class="line"><a name="l00107"></a><span class="lineno">  107</span>&#160;        }</div>
<div class="line"><a name="l00108"></a><span class="lineno">  108</span>&#160;        <span class="keywordflow">catch</span> (<a class="code" href="classOpenMS_1_1Exception_1_1BaseException.html">Exception::BaseException</a> <span class="comment">/*&amp;e*/</span>)</div>
<div class="line"><a name="l00109"></a><span class="lineno">  109</span>&#160;        {</div>
<div class="line"><a name="l00110"></a><span class="lineno">  110</span>&#160;          <span class="keywordflow">throw</span> <a class="code" href="classOpenMS_1_1Exception_1_1ParseError.html">Exception::ParseError</a>(__FILE__, __LINE__, __PRETTY_FUNCTION__, <span class="stringliteral">&quot;&quot;</span>, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;Failed to convert value into a number (line &#39;&quot;</span>) + (i + 1) + <span class="stringliteral">&quot;)&quot;</span>);</div>
<div class="line"><a name="l00111"></a><span class="lineno">  111</span>&#160;        }</div>
<div class="line"><a name="l00112"></a><span class="lineno">  112</span>&#160;        feature_map.push_back(f);</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;    }</div>
<div class="line"><a name="l00115"></a><span class="lineno">  115</span>&#160;</div>
<div class="line"><a name="l00123"></a><span class="lineno">  123</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">typename</span> SpectrumType&gt;</div>
<div class="line"><a name="l00124"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SpecArrayFile.html#aad1400476baaa9e6ff74301f6395c5e8">  124</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1SpecArrayFile.html#aad1400476baaa9e6ff74301f6395c5e8">store</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; filename, <span class="keyword">const</span> SpectrumType &amp; spectrum)<span class="keyword"> const</span></div>
<div class="line"><a name="l00125"></a><span class="lineno">  125</span>&#160;<span class="keyword">    </span>{</div>
<div class="line"><a name="l00126"></a><span class="lineno">  126</span>&#160;      std::cerr &lt;&lt; <span class="stringliteral">&quot;Store() for SpecArrayFile not implemented. Filename was: &quot;</span> &lt;&lt; filename &lt;&lt; <span class="stringliteral">&quot;, spec of size &quot;</span> &lt;&lt; spectrum.size() &lt;&lt; <span class="stringliteral">&quot;\n&quot;</span>;</div>
<div class="line"><a name="l00127"></a><span class="lineno">  127</span>&#160;      <span class="keywordflow">throw</span> <a class="code" href="classOpenMS_1_1Exception_1_1NotImplemented.html">Exception::NotImplemented</a>(__FILE__, __LINE__, __PRETTY_FUNCTION__);</div>
<div class="line"><a name="l00128"></a><span class="lineno">  128</span>&#160;    }</div>
<div class="line"><a name="l00129"></a><span class="lineno">  129</span>&#160;</div>
<div class="line"><a name="l00130"></a><span class="lineno">  130</span>&#160;  };</div>
<div class="line"><a name="l00131"></a><span class="lineno">  131</span>&#160;} <span class="comment">// namespace OpenMS</span></div>
<div class="line"><a name="l00132"></a><span class="lineno">  132</span>&#160;</div>
<div class="line"><a name="l00133"></a><span class="lineno">  133</span>&#160;<span class="preprocessor">#endif // OPENMS_FORMAT_SPECARRAYFILE_H</span></div>
<div class="ttc" id="classOpenMS_1_1MetaInfoInterface_html_a135a7e818125b31198a8a65d9ac7a3d1"><div class="ttname"><a href="classOpenMS_1_1MetaInfoInterface.html#a135a7e818125b31198a8a65d9ac7a3d1">OpenMS::MetaInfoInterface::setMetaValue</a></div><div class="ttdeci">void setMetaValue(const String &amp;name, const DataValue &amp;value)</div><div class="ttdoc">sets the DataValue corresponding to a name </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_1Peak2D_html_a2694f0775c46d9076355cb85d9815425"><div class="ttname"><a href="classOpenMS_1_1Peak2D.html#a2694f0775c46d9076355cb85d9815425">OpenMS::Peak2D::setMZ</a></div><div class="ttdeci">void setMZ(CoordinateType coordinate)</div><div class="ttdoc">Mutable access to the m/z coordinate (index 1) </div><div class="ttdef"><b>Definition:</b> Peak2D.h:197</div></div>
<div class="ttc" id="classOpenMS_1_1SpecArrayFile_html_aad1400476baaa9e6ff74301f6395c5e8"><div class="ttname"><a href="classOpenMS_1_1SpecArrayFile.html#aad1400476baaa9e6ff74301f6395c5e8">OpenMS::SpecArrayFile::store</a></div><div class="ttdeci">void store(const String &amp;filename, const SpectrumType &amp;spectrum) const </div><div class="ttdoc">Stores a featureXML as a SpecArray file. </div><div class="ttdef"><b>Definition:</b> SpecArrayFile.h:124</div></div>
<div class="ttc" id="Feature_8h_html"><div class="ttname"><a href="Feature_8h.html">Feature.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1Peak2D_html_ab875c2479c6cd2a0189e4684bfa4f97d"><div class="ttname"><a href="classOpenMS_1_1Peak2D.html#ab875c2479c6cd2a0189e4684bfa4f97d">OpenMS::Peak2D::setIntensity</a></div><div class="ttdeci">void setIntensity(IntensityType intensity)</div><div class="ttdoc">Non-mutable access to the data point intensity (height) </div><div class="ttdef"><b>Definition:</b> Peak2D.h:167</div></div>
<div class="ttc" id="classOpenMS_1_1SpecArrayFile_html"><div class="ttname"><a href="classOpenMS_1_1SpecArrayFile.html">OpenMS::SpecArrayFile</a></div><div class="ttdoc">File adapter for SpecArray (.pepList) files. </div><div class="ttdef"><b>Definition:</b> SpecArrayFile.h:61</div></div>
<div class="ttc" id="classOpenMS_1_1Peak2D_html_a396c5ebcac2e70f9b9a478bb2456985b"><div class="ttname"><a href="classOpenMS_1_1Peak2D.html#a396c5ebcac2e70f9b9a478bb2456985b">OpenMS::Peak2D::setRT</a></div><div class="ttdeci">void setRT(CoordinateType coordinate)</div><div class="ttdoc">Mutable access to the RT coordinate (index 0) </div><div class="ttdef"><b>Definition:</b> Peak2D.h:209</div></div>
<div class="ttc" id="classOpenMS_1_1Exception_1_1BaseException_html"><div class="ttname"><a href="classOpenMS_1_1Exception_1_1BaseException.html">OpenMS::Exception::BaseException</a></div><div class="ttdoc">Exception base class. </div><div class="ttdef"><b>Definition:</b> Exception.h:90</div></div>
<div class="ttc" id="classOpenMS_1_1Feature_html"><div class="ttname"><a href="classOpenMS_1_1Feature.html">OpenMS::Feature</a></div><div class="ttdoc">An LC-MS feature. </div><div class="ttdef"><b>Definition:</b> Feature.h:66</div></div>
<div class="ttc" id="LogStream_8h_html"><div class="ttname"><a href="LogStream_8h.html">LogStream.h</a></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="TextFile_8h_html"><div class="ttname"><a href="TextFile_8h.html">TextFile.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1BaseFeature_html_ab595724fe9b9eb5d37011f07d90b9e0b"><div class="ttname"><a href="classOpenMS_1_1BaseFeature.html#ab595724fe9b9eb5d37011f07d90b9e0b">OpenMS::BaseFeature::setCharge</a></div><div class="ttdeci">void setCharge(const ChargeType &amp;ch)</div><div class="ttdoc">Set charge state. </div></div>
<div class="ttc" id="classOpenMS_1_1SpecArrayFile_html_aa4e73ca60efa3ca29e203f46b5187c6c"><div class="ttname"><a href="classOpenMS_1_1SpecArrayFile.html#aa4e73ca60efa3ca29e203f46b5187c6c">OpenMS::SpecArrayFile::load</a></div><div class="ttdeci">void load(const String &amp;filename, FeatureMapType &amp;feature_map)</div><div class="ttdoc">Loads a SpecArray file into a featureXML. </div><div class="ttdef"><b>Definition:</b> SpecArrayFile.h:78</div></div>
<div class="ttc" id="Exception_8h_html"><div class="ttname"><a href="Exception_8h.html">Exception.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1String_html_ae580d960e12c7f0ebc5c95931cf39ad5"><div class="ttname"><a href="classOpenMS_1_1String.html#ae580d960e12c7f0ebc5c95931cf39ad5">OpenMS::String::split</a></div><div class="ttdeci">bool split(const char splitter, std::vector&lt; String &gt; &amp;substrings, bool quote_protect=false) const </div><div class="ttdoc">Splits a string into substrings using splitter as delimiter. </div></div>
<div class="ttc" id="classOpenMS_1_1Exception_1_1NotImplemented_html"><div class="ttname"><a href="classOpenMS_1_1Exception_1_1NotImplemented.html">OpenMS::Exception::NotImplemented</a></div><div class="ttdoc">Not implemented exception. </div><div class="ttdef"><b>Definition:</b> Exception.h:437</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_1TextFile_html"><div class="ttname"><a href="classOpenMS_1_1TextFile.html">OpenMS::TextFile</a></div><div class="ttdoc">This class provides some basic file handling methods for text files. </div><div class="ttdef"><b>Definition:</b> TextFile.h:47</div></div>
<div class="ttc" id="classOpenMS_1_1Exception_1_1ParseError_html"><div class="ttname"><a href="classOpenMS_1_1Exception_1_1ParseError.html">OpenMS::Exception::ParseError</a></div><div class="ttdoc">Parse Error exception. </div><div class="ttdef"><b>Definition:</b> Exception.h:608</div></div>
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<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:21 using doxygen 1.8.5</font></TD>
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