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ECL2-2.1.6
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@fcyu fcyu released this 27 Mar 06:47
· 43 commits to master since this release
2.1.6
4925c41

Major Changes

  1. Increase PTM mass decimal point to three. (3325076)
  2. Improve fasta reader. (b4bf5f6)
  3. Preserve the parameter order and print them. (8738c4e)
  4. Improve the String output with String.join(";"). Output all proteins' annotations. (452667e)
  5. Add a databaseType for parsing the header. Add to methods in DbTool. (db9a769, 924f103, 36a1cf1)
  6. Add contaminants.fasta. (9b48fcb)
  7. Delete three unimportant parameters. (72ba36b)
  8. Considering overlapped theoretical fragment ion multiple times.This is what Comet and Xolik do. (8040f53)
  9. Don't half the total score if two sequences are the same. (267408a)
  10. Always single thread in debug mode. (844e3d9)
  11. Add a append_contaminants parameter. (5d2f63a)
  12. Change > delta_c_t to >= delta_c_t. (3aa1733)
  13. Correct MS1 isotope error based on the Mercury method. (6539f32)
  14. Consider the first "M" being cut situation. (b07b34c, e275b43)
  15. Using SQL to reduce the RAM usage. (0d8310d, 1006535, e3fecc5, 807da21)
  16. Delete min_precursor_mass and max_precursor_mass parameters. Delete a unnecessary filter. (b7ef385)

Fixed Bugs:

  1. Fix a bug caused by failing to get the host name. (0c60e56)
  2. Fix a bug that MS level checking is only needed in mzXML format. (72ffd87)
  3. Fix a bug that caused by empty spectrum. (c5325af, a3262e0)
  4. Fix a bug when there is no results in estimating FDR. (63deabe, d368f5e)
  5. Fix a serious bug in CalEValue and improve CalEValue a lot. (418d314, ff49e7e)
  6. Fix a serious bug that may not check the middle bins' combinations. (a4cc349)
  7. Fix a bug in C-C setting. (8398aa4)
  8. Fix a serious bug that does not include any variable modification. (5325db3)

Minor Changes:

  1. Update some library versions and minor improve pom. (449fbff)
  2. Change some default values in the paremeter.def. (60b2d30)
  3. Using ProteomicsLibrary's methods. (c100de8, c3c6c20, 6b88a18, 9442bb5)
  4. Sort the PSMs according to their scores. (382b53a)
  5. Improve the procedure of generating theoretical fragment ions and calculating XCorr. (a212c13)
  6. Delete a debug output. (82cd63f)
  7. Improvement. Assume all advanced parameters are in the parameter.def. Delete unnecessary trim(). (3209614)
  8. Improve logger output. (4c3b840)
  9. Add more explanation to the parameter file. (4ca9035)
Assets 3