Map alignment

OpenMS offers a number of map alignment algorithms. The take several peak or feature maps and transform the retention time axis so that peak/feature positions become comparable.

The classes described in this section can be found in the ANALYSIS/MAPMATCHING folder.

All map alignment algorithms are derived from the common base class MapAlignmentAlgorithm and, thus, share a common interface. That is why only one example (Tutorial_MapAlignment.C) is shown here. Other algorithms can be work accordingly.

First, we load two feature maps:

Int main()
{
  vector<FeatureMap<> > maps;
  maps.resize(2);

  FeatureXMLFile xml_file;
  xml_file.load("data/Tutorial_MapAlignment_1.featureXML", maps[0]);
  xml_file.load("data/Tutorial_MapAlignment_2.featureXML", maps[1]);

Then, we instanciate the algorithm and align the feature maps:

  MapAlignmentAlgorithmPoseClustering algorithm;
  // ... set parameters
  vector<TransformationDescription> transformations;
  algorithm.alignFeatureMaps(maps, transformations);

Finally, the aligned maps are written to files:

  xml_file.store("output/Tutorial_MapAlignment_1.featureXML", maps[0]);
  xml_file.store("output/Tutorial_MapAlignment_2.featureXML", maps[1]);

  return 0;
} //end of main

As an additional output the algorithms return one TransformationDescription per input file. This TransformationDescription describes the transformation that was applied to the retention times.

Note:

In order to align peak maps the method alignPeakMaps has to be used.