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<div class="title">File and DB access </div> </div>
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<div class="textblock"><p>All classes for file and database IO can be found in the <em>FORMAT</em> folder.</p>
<h1><a class="anchor" id="format_file"></a>
File adapter classes</h1>
<p>The interface of most file adapter classes is very similar. They implement a <em>load</em> and a <em>store</em> method, that take a file name and the appropriate data structure.</p>
<p>The following example (Tutorial_FileIO.C) demonstrates the use of <em>MzMLFile</em> and <em>MzXMLFile</em> to convert one format into another using <em>MSExperiment</em> to hold the temporary data: <div class="fragment"><div class="line"><span class="keywordtype">int</span> <a class="code" href="RNPxl_8C.html#a217dbf8b442f20279ea00b898af96f52">main</a>(<span class="keywordtype">int</span> argc, <span class="keyword">const</span> <span class="keywordtype">char</span>** argv)</div>
<div class="line">{</div>
<div class="line"> <span class="keywordflow">if</span> (argc < 2) <span class="keywordflow">return</span> 1;</div>
<div class="line"> <span class="comment">// the path to the data should be given on the command line</span></div>
<div class="line"> String tutorial_data_path(argv[1]);</div>
<div class="line"> </div>
<div class="line"> MzXMLFile mzxml;</div>
<div class="line"> MzMLFile mzml;</div>
<div class="line"></div>
<div class="line"> <span class="comment">// temporary data storage</span></div>
<div class="line"> MSExperiment<Peak1D> map;</div>
<div class="line"></div>
<div class="line"> <span class="comment">// convert MzXML to MzML</span></div>
<div class="line"> mzxml.load(tutorial_data_path + <span class="stringliteral">"/data/Tutorial_FileIO.mzXML"</span>, map);</div>
<div class="line"> mzml.store(<span class="stringliteral">"Tutorial_FileIO.mzML"</span>, map);</div>
<div class="line"></div>
<div class="line"> <span class="keywordflow">return</span> 0;</div>
<div class="line">} <span class="comment">//end of main</span></div>
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<dl class="section user"><dt>FileHandler</dt><dd>In order to make the handling of different file types easier, the class <em>FileHandler</em> can be used. It loads a file into the appropriate data structure independently of the file type. The file type is determined from the file extension or the file contents: <div class="fragment"><div class="line">MSExperiment<> in;</div>
<div class="line">FileHandler handler();</div>
<div class="line">handler.loadExperiment(<span class="stringliteral">"input.mzML"</span>,in);</div>
</div><!-- fragment --></dd></dl>
<h1><a class="anchor" id="format_db"></a>
DB access</h1>
<p>For database access, the class <em>DBAdapter</em> is used. As its interface is very similar to the interface of the file adapters, no example is shown here.</p>
<h1><a class="anchor" id="format_options"></a>
PeakFileOptions</h1>
<p>In order to have more control over loading data from files or databases, most adapters can be configured using <em>PeakFileOptions</em>. The following options are available:</p>
<ul>
<li>only a specific retention time range is loaded</li>
<li>only a specific mass-to.charge ratio range is loaded</li>
<li>only a specific intensity range is loaded</li>
<li>only spectra with a given MS level are loaded</li>
<li>only meta data of the whole experiment is loaded (<em>ExperimentalSettings</em>) </li>
</ul>
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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 11:19:24 using doxygen 1.8.5</font></TD>
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