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<dt><a class="anchor" id="_deprecated000005"></a>Page <a class="el" href="TOPP_DBExporter.html">DBExporter</a> </dt>
<dd>Deprecated in <a class="el" href="namespaceOpenMS.html" title="Main OpenMS namespace. ">OpenMS</a> 1.9 </dd>
<dt><a class="anchor" id="_deprecated000006"></a>Page <a class="el" href="TOPP_DBImporter.html">DBImporter</a> </dt>
<dd>Deprecated in <a class="el" href="namespaceOpenMS.html" title="Main OpenMS namespace. ">OpenMS</a> 1.9 </dd>
<dt><a class="anchor" id="_deprecated000003"></a>Class <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmSimple.html">FeatureFinderAlgorithmSimple< PeakType, FeatureType ></a> </dt>
<dd>Deprecated in <a class="el" href="namespaceOpenMS.html" title="Main OpenMS namespace. ">OpenMS</a> 1.7. </dd>
<dt><a class="anchor" id="_deprecated000004"></a>Class <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmSimplest.html">FeatureFinderAlgorithmSimplest< PeakType, FeatureType ></a> </dt>
<dd>Deprecated in <a class="el" href="namespaceOpenMS.html" title="Main OpenMS namespace. ">OpenMS</a> 1.7. </dd>
<dt><a class="anchor" id="_deprecated000001"></a>Class <a class="el" href="classOpenMS_1_1FeatureGroupingAlgorithmIdentification.html">FeatureGroupingAlgorithmIdentification</a> </dt>
<dd>Deprecated in <a class="el" href="namespaceOpenMS.html" title="Main OpenMS namespace. ">OpenMS</a> 1.7. </dd>
<dt><a class="anchor" id="_deprecated000007"></a>Page <a class="el" href="TOPP_IDMapper.html">IDMapper</a> </dt>
<dd>The parameter handling of this tool has been reworked. For greater consistency with other tools, the parameters <code>rt_delta</code> and <code>mz_delta</code> have been renamed to <code>rt_tolerance</code> and <code>mz_tolerance</code>. The possible values of the <code>mz_reference</code> parameter have also been renamed. The default value of <code>mz_tolerance</code> has been increased from 1 ppm to a more realistic 20 ppm.<br/>
Most importantly, the <code>use_centroids</code> parameter from previous versions has been split into two parameters, <code>feature:use_centroid_rt</code> and <code>feature:use_centroid_mz</code>. In <a class="el" href="namespaceOpenMS.html" title="Main OpenMS namespace. ">OpenMS</a> 1.6, peptide identifications would be matched only against monoisotopic mass traces of features if <code>mz_reference</code> was <code>PeptideMass</code>; otherwise, all mass traces would be used. This implicit behaviour has been abandoned, you can now explicitly control it with the <code>feature:use_centroid_mz</code> parameter. <code>feature:use_centroid_mz</code> does not take into account m/z deviations in the monoisotopic mass trace, but this can be compensated by increasing <code>mz_tolerance</code>. The new implementation should work correctly even if the monoisotopic mass trace itself was not detected. </dd>
<dt><a class="anchor" id="_deprecated000002"></a>Class <a class="el" href="classOpenMS_1_1MascotInfile.html">MascotInfile</a> </dt>
<dd>Use <a class="el" href="MascotGenericFile_8h.html">MascotGenericFile.h</a> instead, which uses DefaultParamHandler, is more up to date and avoids weird behaviors of this class (especially in terms of MIME boundaries when writing MGF....</dd>
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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 11:19:25 using doxygen 1.8.5</font></TD>
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