[TEST] add modification test

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@505 db641661-14cc-1e01-c2f8-e77ac6f8a696
[FIX] add encapsulation

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@506 db641661-14cc-1e01-c2f8-e77ac6f8a696
[FEATURE] add assertions and pre/post conditions

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@507 db641661-14cc-1e01-c2f8-e77ac6f8a696
[FEATURE,REFACTOR] PrecursorGroup: add PrecursorGroup object into hierarchy

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@508 db641661-14cc-1e01-c2f8-e77ac6f8a696
[REFACTOR] PrecursorGroup: add Multipeptide

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@509 db641661-14cc-1e01-c2f8-e77ac6f8a696
[REFACTOR] PrecursorGroup: add MRExperiment

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@510 db641661-14cc-1e01-c2f8-e77ac6f8a696
[REFACTOR] PrecursorGroup: add SplineAligner

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@511 db641661-14cc-1e01-c2f8-e77ac6f8a696
[REFACTOR] PrecursorGroup: adopt spline aligner

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@512 db641661-14cc-1e01-c2f8-e77ac6f8a696
[REFACTOR] PrecursorGroup: add AlignmentAlgorithm

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@513 db641661-14cc-1e01-c2f8-e77ac6f8a696
[REFACTOR] PrecursorGroup: add FDRParameterEstimation

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@514 db641661-14cc-1e01-c2f8-e77ac6f8a696
[FIX,REFACTOR] PrecursorGroup: adopt the matrix outfile code

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@515 db641661-14cc-1e01-c2f8-e77ac6f8a696
[FIX,REFACTOR] PrecursorGroup: fix executable feature alignment

- adopt feature_alignment to the new object structure

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@516 db641661-14cc-1e01-c2f8-e77ac6f8a696
[TEST,REFACTOR] PrecursorGroup: fix integration test

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@517 db641661-14cc-1e01-c2f8-e77ac6f8a696
[REFACTOR,FIX] PrecursorGroup: check and throw error if more than 1 pg/run

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@518 db641661-14cc-1e01-c2f8-e77ac6f8a696
[NOP] data structure fixes

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@519 db641661-14cc-1e01-c2f8-e77ac6f8a696
[REFACTOR,TEST] update tests

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@520 db641661-14cc-1e01-c2f8-e77ac6f8a696
[REFACTOR,TEST] update tests

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@521 db641661-14cc-1e01-c2f8-e77ac6f8a696
[FEATURE] adopt requant script to heavy/light

- allow precursor group pairs of heavy light and impute borders
  correctly from the paired isotopic channel if available

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@522 db641661-14cc-1e01-c2f8-e77ac6f8a696
[TEST] add test for requant with isotopic patterns

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@523 db641661-14cc-1e01-c2f8-e77ac6f8a696
[REFACTOR] PrecursorGroup: change insert function

- insert now works differently, cannot append directly to a precursor
  any more

git-svn-id: https://msproteomicstools.googlecode.com/svn/trunk@524 db641661-14cc-1e01-c2f8-e77ac6f8a696