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<TITLE>How meta data is stored</TITLE>
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<div class="title">How meta data is stored </div> </div>
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<div class="textblock"><p>The meta informations about an HPLC-MS experiment are stored in <em>ExperimentalSettings</em> and <em>SpectrumSettings</em>. All information that is not covered by these classes can be stored in the type-name-value datastructure <em>MetaInfo</em>. All classes described in this section can be found in the <em>METADATA</em> folder.</p>
<h1><a class="anchor" id="metadata_metainfo"></a>
MetaInfo</h1>
<p><em>DataValue</em> is a data structure that can store any numerical or string information. It also supports casting of the stored value back to its original type.</p>
<p><em>MetaInfo</em> is used to easily store information of any type, that does not fit into the the other classes. It implements type-name-value triplets. The main datastructure is an associative container that stores <em>DataValue</em> instances as values associated to string keys. Internally, the string keys are converted to integer keys for performance resaons i.e. a <em>map<UInt,DataValue></em> is used.</p>
<p>The <em>MetaInfoRegistry</em> associates the string keys used in <em>MetaValue</em> with the integer values that are used for internal storage. The <em>MetaInfoRegistry</em> is a singleton.</p>
<p>If you want a class to have a <em>MetaInfo</em> member, simply derive it from <em>MetaInfoInterface</em>. This class provides a <em>MetaInfo</em> member and the interface to access it.</p>
<div class="image">
<img src="MetaInfo.png" alt="MetaInfo.png"/>
<div class="caption">
The classes involved in meta information storage</div></div>
<p>The following example (Tutorial_MetaInfo.C) shows how to use <em>Metadata</em>. We can simply set values for the string keys, and <em>setMetaValue</em> registers these names automatically. In order to access the values, we can either use the registered name or the index of the name. The <em>getMetaValue</em> method returns a <em>DataValue</em>, which has to be casted to the right type. If you do not know the type, you can use the <em>DataValue::valueType()</em> method. <div class="fragment"><div class="line"><a class="code" href="classInt.html">Int</a> <a class="code" href="RNPxl_8C.html#a217dbf8b442f20279ea00b898af96f52">main</a>()</div>
<div class="line">{</div>
<div class="line"> MetaInfoInterface info;</div>
<div class="line"></div>
<div class="line"> <span class="comment">//insert meta data</span></div>
<div class="line"> info.setMetaValue(<span class="stringliteral">"color"</span>, String(<span class="stringliteral">"#ff0000"</span>));</div>
<div class="line"> info.setMetaValue(<span class="stringliteral">"id"</span>, 112131415);</div>
<div class="line"></div>
<div class="line"> <span class="comment">//access id by index</span></div>
<div class="line"> <a class="code" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a> id_index = info.metaRegistry().getIndex(<span class="stringliteral">"id"</span>);</div>
<div class="line"> cout << <span class="stringliteral">"id : "</span> << (<a class="code" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a>)(info.getMetaValue(id_index)) << endl;</div>
<div class="line"> <span class="comment">//access color by name</span></div>
<div class="line"> cout << <span class="stringliteral">"color: "</span> << (String)(info.getMetaValue(<span class="stringliteral">"color"</span>)) << endl;</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>
</div><!-- fragment --></p>
<h1><a class="anchor" id="metadata_experiment"></a>
Meta data of a map</h1>
<p>This class holds meta information about the experiment that is valid for the whole experiment:</p>
<ul>
<li>sample description</li>
<li>source files</li>
<li>contact persons</li>
<li>MS instrument</li>
<li>HPLC settings</li>
<li>protein identifications</li>
</ul>
<div class="image">
<img src="ExperimentalSettings.png" alt="ExperimentalSettings.png"/>
<div class="caption">
Map meta information</div></div>
<h1><a class="anchor" id="metadata_spectrum"></a>
Meta data of a spectrum</h1>
<p>This class contains meta information about settings specific to one spectrum:</p>
<ul>
<li>spectrum-specific instrument settings</li>
<li>source file</li>
<li>information on the acquisition</li>
<li>precursor information (e.g. for MS/MS spectra)</li>
<li>product information (e.g. for SRM spectra)</li>
<li>processing performed on the data</li>
<li>peptide identifications</li>
</ul>
<div class="image">
<img src="SpectrumSettings.png" alt="SpectrumSettings.png"/>
<div class="caption">
Spectrum meta information</div></div>
<h1><a class="anchor" id="metadata_peaks"></a>
Meta data associated to peaks</h1>
<p>If you want to annotate the peaks or raw data points in your spectra with meta information, there are three different ways to do this with different advantages and disadvantages.</p>
<p>If each peak is annotated with the same type of information (e.g. width of a peak):</p>
<ul>
<li>Use the meta data arrays provided by MSSpectrum (recommended)<ul>
<li>Advantages: Independent of peak type, information automatically stored in mzML files</li>
<li>Disadvantages: Information can be accessed through index only</li>
</ul>
</li>
<li>Derive a new peak type that contains members for the additional information<ul>
<li>Advantages: Very fast</li>
<li>Disadvantages: Information not automatically stored in mzML files, Custom peak type are not supported by all algorithms</li>
</ul>
</li>
</ul>
<p>If you need to annotate only a small subset of the peaks with meta information:</p>
<ul>
<li>Use the MetaInfoInterface of RichPeak1D<ul>
<li>Advantages: Each peak can be annotated with individual information</li>
<li>Disadvantages: Quite slow, Information not automatically stored in mzML files </li>
</ul>
</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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