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<div class="textblock"><dl class="reflist">
<dt><a class="anchor" id="_todo000007"></a>Class <a class="el" href="classOpenMS_1_1ConsensusXMLFile.html">ConsensusXMLFile</a> </dt>
<dd>Take care that unique ids are assigned properly by TOPP tools before calling ConsensusXMLFile::store(). There will be a message on LOG_INFO but we will make no attempt to fix the problem in this class. (all developers) </dd>
<dt><a class="anchor" id="_todo000008"></a>Class <a class="el" href="classOpenMS_1_1DBAdapter.html">DBAdapter</a> </dt>
<dd><p class="startdd">Add DataProcessing to MetaInfoDescription (Hiwi, Mathias) </p>
<p>Check if test is really complete (Hiwi, Mathias) </p>
<p>Check that all values are quoted (Hiwi, Mathias) </p>
<p class="enddd">Implement StringDataArray and IntegerDataArray of spectrum (Hiwi, Mathias) </p>
</dd>
<dt><a class="anchor" id="_todo000001"></a>Class <a class="el" href="classOpenMS_1_1FalseDiscoveryRate.html">FalseDiscoveryRate</a> </dt>
<dd>implement combined searches properly (Andreas) </dd>
<dt><a class="anchor" id="_todo000019"></a>Member <a class="el" href="classOpenMS_1_1FeatureFinder.html#a001d4adf21652ff6cdd58efe56e4fb1c">FeatureFinder::run</a> (const String &algorithm_name, MSExperiment< PeakType > &input_map, FeatureMap< FeatureType > &features, const Param &param, const FeatureMap< FeatureType > &seeds)</dt>
<dd>that happens sometimes using IsotopeWaveletFeatureFinder (Rene, Marc, Andreas, Clemens) </dd>
<dt><a class="anchor" id="_todo000020"></a>Class <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html">FeatureFinderAlgorithmPicked< PeakType, FeatureType ></a> </dt>
<dd><p class="startdd">Fix output in parallel mode, change assignment of charges to threads, add parallel TOPP test (Marc) </p>
<p class="enddd">Implement user-specified seed lists support (Marc) </p>
</dd>
<dt><a class="anchor" id="_todo000009"></a>Class <a class="el" href="classOpenMS_1_1FeatureXMLFile.html">FeatureXMLFile</a> </dt>
<dd>Take care that unique ids are assigned properly by TOPP tools before calling FeatureXMLFile::store(). There will be a message on LOG_INFO but we will make no attempt to fix the problem in this class. (all developers) </dd>
<dt><a class="anchor" id="_todo000031"></a>Page <a class="el" href="TOPP_FileFilter.html">FileFilter</a> </dt>
<dd>add tests for selecting modes (port remove modes) (Andreas) </dd>
<dt><a class="anchor" id="_todo000037"></a>Group <a class="el" href="group__FileIO.html">FileIO</a> </dt>
<dd><p class="startdd">Implement reading of pepXML and protXML (Andreas) </p>
<p class="enddd">Allow reading of zipped XML files (David, Hiwi) </p>
</dd>
<dt><a class="anchor" id="_todo000021"></a>Class <a class="el" href="classOpenMS_1_1GaussTraceFitter.html">GaussTraceFitter< PeakType ></a> </dt>
<dd>More docu </dd>
<dt><a class="anchor" id="_todo000014"></a>Class <a class="el" href="classOpenMS_1_1Identification.html">Identification</a> </dt>
<dd>docu (Andreas) </dd>
<dt><a class="anchor" id="_todo000015"></a>Class <a class="el" href="classOpenMS_1_1IdentificationHit.html">IdentificationHit</a> </dt>
<dd>docu (Andreas) </dd>
<dt><a class="anchor" id="_todo000003"></a>Class <a class="el" href="classOpenMS_1_1InclusionExclusionList.html">InclusionExclusionList</a> </dt>
<dd>allow modifications (fixed?) </dd>
<dt><a class="anchor" id="_todo000032"></a>Page <a class="el" href="TOPP_InspectAdapter.html">InspectAdapter</a> </dt>
<dd>rewrite the Adapter! It uses old formats and coding style, e.g. mzData input allowed, no input restrictions, manual (unneccessary file checking of input files) etc... + the interface is not convenient, etc ... </dd>
<dt><a class="anchor" id="_todo000010"></a>Class <a class="el" href="classOpenMS_1_1InspectOutfile.html">InspectOutfile</a> </dt>
<dd>Handle Modifications (Andreas) </dd>
<dt><a class="anchor" id="_todo000006"></a>Class <a class="el" href="classOpenMS_1_1IsotopeMarker.html">IsotopeMarker</a> </dt>
<dd>implement a real isotope marking here with isotopedistributions and fitting (Andreas) </dd>
<dt><a class="anchor" id="_todo000002"></a>Class <a class="el" href="classOpenMS_1_1LabeledPairFinder.html">LabeledPairFinder</a> </dt>
<dd><p class="startdd">Implement support for labled MRM experiments, Q1 m/z value and charges. (Andreas) </p>
<p class="enddd">Implement support for more than one mass delta, e.g. from missed cleavages and so on (Andreas) </p>
</dd>
<dt><a class="anchor" id="_todo000033"></a>Page <a class="el" href="TOPP_MascotAdapter.html">MascotAdapter</a> </dt>
<dd>This adapter is using antiquated internal methods and needs to be updated! E.g. use <a class="el" href="MascotGenericFile_8h.html">MascotGenericFile.h</a> instead of <a class="el" href="MascotInfile_8h.html">MascotInfile.h</a>.... </dd>
<dt><a class="anchor" id="_todo000022"></a>Class <a class="el" href="classOpenMS_1_1ModelFitter.html">ModelFitter< PeakType, FeatureType ></a> </dt>
<dd>Fix problem with other peak types than Peak1D and enable the respective tests for FeatureFinderAlgorithmSimple, FeatureFinderAlgorithmSimplest, FeatureFinderAlgorithmWavelet (Clemens) </dd>
<dt><a class="anchor" id="_todo000011"></a>Class <a class="el" href="classOpenMS_1_1MzMLFile.html">MzMLFile</a> </dt>
<dd>Implement chromatograms (Andreas) </dd>
<dt><a class="anchor" id="_todo000016"></a>Class <a class="el" href="classOpenMS_1_1PeptideEvidence.html">PeptideEvidence</a> </dt>
<dd>implement CVParam </dd>
<dt><a class="anchor" id="_todo000034"></a>Page <a class="el" href="TOPP_PILISIdentification.html">PILISIdentification</a> </dt>
<dd>Check for missing precursors (Hiwi) </dd>
<dt><a class="anchor" id="_todo000023"></a>Class <a class="el" href="classOpenMS_1_1ProductModel.html">ProductModel< D ></a> </dt>
<dd>This class provides new member functions, which makes Factory<<a class="el" href="classOpenMS_1_1BaseModel.html">BaseModel<2></a> >::create("ProductModel2D") pretty much useless! (Clemens) </dd>
<dt><a class="anchor" id="_todo000017"></a>Class <a class="el" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a> </dt>
<dd>Add MetaInfoInterface to modifications => update IdXMLFile and ProteinIdentificationVisualizer (Andreas) </dd>
<dt><a class="anchor" id="_todo000012"></a>Class <a class="el" href="classOpenMS_1_1ProtXMLFile.html">ProtXMLFile</a> </dt>
<dd>Document which metavalues of Protein/PeptideHit are filled when reading ProtXML (Chris) </dd>
<dt><a class="anchor" id="_todo000005"></a>Member <a class="el" href="classOpenMS_1_1Residue.html#a7651af21f9cf8ed6445415903fc6cb48abcb96a1dd10fd595ff7d6789848b7b9c">Residue::SizeOfResidueType</a> </dt>
<dd>add c+1, z+1, z+2 ion types (Andreas) </dd>
<dt><a class="anchor" id="_todo000035"></a>Page <a class="el" href="TOPP_RTPredict.html">RTPredict</a> </dt>
<dd>This need serious clean up! Combining certain input and output options will result in strange behaviour, especially when using text output/input. </dd>
<dt><a class="anchor" id="_todo000036"></a>Page <a class="el" href="TOPP_SequestAdapter.html">SequestAdapter</a> </dt>
<dd>Check for missing precursors (Andreas) </dd>
<dt><a class="anchor" id="_todo000013"></a>Class <a class="el" href="classOpenMS_1_1SequestOutfile.html">SequestOutfile</a> </dt>
<dd><p class="startdd">Handle Modifications (Andreas) </p>
<p class="enddd">Complete rewrite of the parser (and those of InsPecT and PepNovo), the code is bullshit... (Andreas) </p>
</dd>
<dt><a class="anchor" id="_todo000028"></a>Class <a class="el" href="classOpenMS_1_1Spectrum1DCanvas.html">Spectrum1DCanvas</a> </dt>
<dd>Use spectrum StringDataArray with name 'label' for peak annotations (Hiwi, Johannes) </dd>
<dt><a class="anchor" id="_todo000029"></a>Class <a class="el" href="classOpenMS_1_1SpectrumCanvas.html">SpectrumCanvas</a> </dt>
<dd>Allow reordering the layer list by drag-and-drop (Hiwi, Johannes) </dd>
<dt><a class="anchor" id="_todo000018"></a>Class <a class="el" href="classOpenMS_1_1SpectrumIdentification.html">SpectrumIdentification</a> </dt>
<dd>docu (Andreas) </dd>
<dt><a class="anchor" id="_todo000030"></a>Class <a class="el" href="classOpenMS_1_1SpectrumWidget.html">SpectrumWidget</a> </dt>
<dd>Add support to store the displayed data as SVG image (HiWi) </dd>
<dt><a class="anchor" id="_todo000004"></a>Class <a class="el" href="classOpenMS_1_1TOPPBase.html">TOPPBase</a> </dt>
<dd>: replace writeLog_, writeDebug_ with a logger concept we'd need something like -VLevels [LOGGERS] to specify which loggers shall print something the '-log' flag should clone all output to the log-file (maybe with custom [LOGGERS]), which can either be specified directly or is equal to '-out' (if present) with a ".log" suffix maybe a new LOGGER type (TOPP), which is only usable on TOPP level? </dd>
<dt><a class="anchor" id="_todo000027"></a>Class <a class="el" href="classOpenMS_1_1TOPPViewBase.html">TOPPViewBase</a> </dt>
<dd>Add TOPPView live-tutorial (Stephan, Marc) </dd>
<dt><a class="anchor" id="_todo000024"></a>Class <a class="el" href="classOpenMS_1_1TraceFitter.html">TraceFitter< PeakType ></a> </dt>
<dd>docu needs update </dd>
<dt><a class="anchor" id="_todo000025"></a>Member <a class="el" href="classOpenMS_1_1TraceFitter.html#a642bbbd0de05e84147e701bfeaf188a2">TraceFitter< PeakType >::getFeatureIntensityContribution</a> ()=0</dt>
<dd>docu needs update </dd>
<dt><a class="anchor" id="_todo000026"></a>Class <a class="el" href="classOpenMS_1_1TwoDOptimization.html">TwoDOptimization</a> </dt>
<dd>Works only with defined types due to pointers to the data in the optimization namespace! Change that or remove templates (Alexandra)</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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