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<div class="title">Auxiliary datastructures </div> </div>
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<div class="textblock"><p>This section contains a short introduction to three datastructures you will definitely need when programming with OpenMS. The datastructures module of the class documentation contains many more classes, which are not mentioned here in detail. The classes described in this section can be found in the <em>DATASTRUCTURES</em> folder.</p>
<h1><a class="anchor" id="datastructures_string"></a>
The OpenMS string implementation</h1>
<p>The OpenMS string implementation <em>String</em> is based on the STL <em>std::string</em>. In order to make the OpenMS string class more convenient, a lot of methods have been implemented in addition to the methods provided by the base class. A selection of the added functionaliy is given here:</p>
<ul>
<li>Checking for a substring (suffix, prefix, substring, char)</li>
<li>Extracting a substring (suffix, prefix, substring)</li>
<li>Trimming (left, right, both sides)</li>
<li>Concatenation of string and other primitive types with <em>operator+</em> </li>
<li>Construction from QString and conversion to QString</li>
</ul>
<h1><a class="anchor" id="datastructures_dposition"></a>
D-dimensional coordinates</h1>
<p>Many OpenMS classes, especially the kernel classes, need to store some kind of d-dimensional coordinates. The template class <em>DPosition</em> is used for that purpose. The interface of DPosition is pretty straightforward. The operator[] is used to access the coordinate of the different dimensions. The dimensionality is stored in the enum value <em>DIMENSION</em>. The following example (Tutorial_DPosition.C) shows how to print a DPosition to the standard output stream.</p>
<p>First we need to include the header file for <em>DPosition</em> and <em>iostream</em>. Then we import all the OpenMS symbols to the scope with the <em>using</em> directive. <div class="fragment"><div class="line"><span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><span class="comment">// OpenMS -- Open-Source Mass Spectrometry</span></div>
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<div class="line"><span class="comment">// ETH Zurich, and Freie Universitaet Berlin 2002-2013.</span></div>
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<div class="line"><span class="comment">// notice, this list of conditions and the following disclaimer.</span></div>
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<div class="line"></div>
<div class="line"><span class="preprocessor">#include <<a class="code" href="DPosition_8h.html">OpenMS/DATASTRUCTURES/DPosition.h</a>></span></div>
<div class="line"><span class="preprocessor">#include <iostream></span></div>
<div class="line"></div>
<div class="line"><span class="keyword">using namespace </span>OpenMS;</div>
</div><!-- fragment --> The first commands in the main method initialize a 2-dimensional <em>DPosition</em> : <div class="fragment"><div class="line"></div>
<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"> DPosition<2> pos;</div>
<div class="line"> pos[0] = 8.15;</div>
<div class="line"> pos[1] = 47.11;</div>
</div><!-- fragment --> Finally we print the content of the DPosition to the standard output stream: <div class="fragment"><div class="line"></div>
<div class="line"> <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i < DPosition<2>::DIMENSION; ++i)</div>
<div class="line"> {</div>
<div class="line"> std::cout << <span class="stringliteral">"Dimension "</span> << i << <span class="stringliteral">": "</span> << pos[i] << std::endl;</div>
<div class="line"> }</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>
<p>The output of our first little OpenMS program is the following: </p>
<div class="fragment"><div class="line">Dimension 0: 8.15</div>
<div class="line">Dimension 1: 47.11</div>
</div><!-- fragment --><h1><a class="anchor" id="datastructures_drange"></a>
D-dimensional ranges</h1>
<p>Another important datastructure we need to look at in detail is <em>DRange</em>. It defines a d-dimensional, half-open interval through its two <em>DPosition</em> members. These members are accessed by the <em>minPosition()</em> and <em>maxPosition()</em> methods and can be set by the <em>setMin()</em> and <em>setMax()</em> methods.</p>
<p>DRange maintains the invariant that <em>minPosition()</em> is geometrically less or equal to <em>maxPosition()</em>, i.e. <img class="formulaInl" alt="$ minPosition()[x] \le maxPosition()[x]$" src="form_101.png"/> for each dimension <em>x</em>. The following example (Tutorial_DRange.C) demonstrates this behavior.</p>
<p>This time, we skip everything before the main method. In the main method, we create a range and assign values to <em>min</em> and <em>max</em>. Note that the the minimum value of the first dimension is larger than the maximum value. <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"> DRange<2> range;</div>
<div class="line"> range.setMin(DPosition<2>(2.0, 3.0));</div>
<div class="line"> range.setMax(DPosition<2>(1.0, 5.0));</div>
</div><!-- fragment --> Then we print the content of <em>range</em> : <div class="fragment"><div class="line"></div>
<div class="line"> <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a> i = 0; i < DRange<2>::DIMENSION; ++i)</div>
<div class="line"> {</div>
<div class="line"> std::cout << <span class="stringliteral">"min "</span> << i << <span class="stringliteral">": "</span> << range.minPosition()[i] << std::endl;</div>
<div class="line"> std::cout << <span class="stringliteral">"max "</span> << i << <span class="stringliteral">": "</span> << range.maxPosition()[i] << std::endl;</div>
<div class="line"> }</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>
<p>The output is: </p>
<div class="fragment"><div class="line">min 0: 1</div>
<div class="line">max 0: 1</div>
<div class="line">min 1: 3</div>
<div class="line">max 1: 5</div>
</div><!-- fragment --><p> As you can see, the minimum value of dimension one was adjusted in order to make the maximum of <em>1</em> conform with the invariant.</p>
<p><em>DIntervalBase</em> is the closed interval counterpart (and base class) of <em>DRange</em>. Another class derived from <em>DIntervalBase</em> is <em>DBoundingBox</em>. It also represents a closed interval, but differs in the methods. Please have a look at the class documentation for details.</p>
<h1><a class="anchor" id="datastructures_param"></a>
Param</h1>
<p>Most algorithms of OpenMS and some of the TOPP tools have many parameters. The parameters are stored in instances of <em>Param</em>. This class is similar to a Windows INI file. The actual parameters (type, name and value) are stored in sections. Sections can contain parameters and sub-sections, which leads to a tree-like structure. The values are stored in <em>DataValue</em>. <br/>
Parameter names are given as a string including the sections and subsections in which ':' is used as a delimiter.</p>
<p>The following example (Tutorial_Param.C) shows how a file description is given. <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"> Param param;</div>
<div class="line"></div>
<div class="line"> param.setValue(<span class="stringliteral">"file:name"</span>, <span class="stringliteral">"test.xml"</span>);</div>
<div class="line"> param.setValue(<span class="stringliteral">"file:size(MB)"</span>, 572.3);</div>
<div class="line"> param.setValue(<span class="stringliteral">"file:data:min_int"</span>, 0);</div>
<div class="line"> param.setValue(<span class="stringliteral">"file:data:max_int"</span>, 16459);</div>
<div class="line"></div>
<div class="line"> cout << <span class="stringliteral">"Name : "</span> << (String)(param.getValue(<span class="stringliteral">"file:name"</span>)) << endl;</div>
<div class="line"> cout << <span class="stringliteral">"Size : "</span> << (<a class="code" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a>)(param.getValue(<span class="stringliteral">"file:size(MB)"</span>)) << endl;</div>
<div class="line"> cout << <span class="stringliteral">"Min int: "</span> << (<a class="code" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a>)(param.getValue(<span class="stringliteral">"file:data:min_int"</span>)) << endl;</div>
<div class="line"> cout << <span class="stringliteral">"Max int: "</span> << (<a class="code" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a>)(param.getValue(<span class="stringliteral">"file:data:max_int"</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>
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