OpenMS/OpenMS — pull request #1087 by lars20070 (2014-11-30 10:10:59+00:00)
Title: centroided input data for FeatureFinderMultiplex

This pull request extends the functionality of FeatureFinderMultiplex by allowing centroided data as input. The major code changes were made in the filtering part of the algorithm. MultiplexFiltering is now a base class from which MultiplexFilteringCentroided and MultiplexFilteringProfile are derived. The FeatureFinderMultiplex parameters remain unchanged; the type of input data is detected automatically.

First tests show that the differences of running FeatureFinderMultiplex on profile or centroided data are minimal. Run time decreases by 12%. The number of peptide pairs increases by 0.7%. The standard deviation of the fold changes in a fixed ratio experiment increase by 0.9%. The positions of the peptide pairs are very similar too, see screenshots for profile (green) and centroided (red).

![profile](https://cloud.githubusercontent.com/assets/6149805/5237381/0803cb76-7881-11e4-813b-e11daad25b22.png)
![centroided](https://cloud.githubusercontent.com/assets/6149805/5237382/12e26b10-7881-11e4-9a18-d4e5285cd388.png)
![profilecentroided](https://cloud.githubusercontent.com/assets/6149805/5237384/18400ef0-7881-11e4-8bf2-0615df1b6533.png)
![plot_profile](https://cloud.githubusercontent.com/assets/6149805/5237393/6052f8e2-7881-11e4-8001-13e7d71a918c.png)
![plot_centroided](https://cloud.githubusercontent.com/assets/6149805/5237394/650d1d0e-7881-11e4-8a30-4ccba8646192.png)