[TEST] also test matrix output

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@197 db641661-14cc-1e01-c2f8-e77ac6f8a696
[INTERNAL] move matrix output

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@198 db641661-14cc-1e01-c2f8-e77ac6f8a696
[INTERNAL] refactoring

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@199 db641661-14cc-1e01-c2f8-e77ac6f8a696
[FIX] select all aligned peakgroups

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@200 db641661-14cc-1e01-c2f8-e77ac6f8a696
[FEATURE] allow to write out matrix file

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@201 db641661-14cc-1e01-c2f8-e77ac6f8a696
[INTERNAL] better documentation and interface for TransformationCollection

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@202 db641661-14cc-1e01-c2f8-e77ac6f8a696
[FEATURE] add feature to calculate new border by mean or maximal width

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@203 db641661-14cc-1e01-c2f8-e77ac6f8a696
[FEATURE] fill more rows in output, consider SWATH overlap when selecting the window

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@204 db641661-14cc-1e01-c2f8-e77ac6f8a696
spectrast_updateiRTs.py > modified the script to rename the output file as FILE_iRT.sptxt instead of overwriting the input FILE.sptxt 

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@205 db641661-14cc-1e01-c2f8-e77ac6f8a696
[FEATURE] add readfilter to only read part of the data

- add ReadFilter to only read data with a d_score above a certain
  threshold (callable object which is evaluated while parsing)
- Multipeptide now explicitly requires to know how many runs there are
  (since it might not have a peptide for each run)

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@206 db641661-14cc-1e01-c2f8-e77ac6f8a696
[TEST] add test for best_overall method, cleanup test

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@207 db641661-14cc-1e01-c2f8-e77ac6f8a696
[FIX] bugfix for outlier detection

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@208 db641661-14cc-1e01-c2f8-e77ac6f8a696
[INTERNAL] refactor alignment algorithm

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@209 db641661-14cc-1e01-c2f8-e77ac6f8a696
[FEATURE] add high confidence run filtering

- also rework the output section

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@210 db641661-14cc-1e01-c2f8-e77ac6f8a696
[INTERNAL] refactor, move code into lib

- new AlignmentAlgorithm.py
- new MRExperiment.py
- new Multipeptide.py
- new SplineAligner.py

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@211 db641661-14cc-1e01-c2f8-e77ac6f8a696
[NOP] remove R warnings

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@212 db641661-14cc-1e01-c2f8-e77ac6f8a696
[INTERNAL] store initial fdr cutoff for later computation

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@213 db641661-14cc-1e01-c2f8-e77ac6f8a696
[FIX] check for empty groups, check input for trafo

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@214 db641661-14cc-1e01-c2f8-e77ac6f8a696
[FEATURE] Parameter estimation

- feature to estimate the FDR cutoff parameter

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@215 db641661-14cc-1e01-c2f8-e77ac6f8a696
[FIX] change filter to reflect its description (breaking change)

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@216 db641661-14cc-1e01-c2f8-e77ac6f8a696