Releases
2.1.6
fcyu
released this
27 Mar 06:47
Major Changes
Increase PTM mass decimal point to three. (3325076 )
Improve fasta reader. (b4bf5f6 )
Preserve the parameter order and print them. (8738c4e )
Improve the String output with String.join(";"). Output all proteins' annotations. (452667e )
Add a databaseType for parsing the header. Add to methods in DbTool. (db9a769 , 924f103 , 36a1cf1 )
Add contaminants.fasta. (9b48fcb )
Delete three unimportant parameters. (72ba36b )
Considering overlapped theoretical fragment ion multiple times.This is what Comet and Xolik do. (8040f53 )
Don't half the total score if two sequences are the same. (267408a )
Always single thread in debug mode. (844e3d9 )
Add a append_contaminants parameter. (5d2f63a )
Change > delta_c_t to >= delta_c_t. (3aa1733 )
Correct MS1 isotope error based on the Mercury method. (6539f32 )
Consider the first "M" being cut situation. (b07b34c , e275b43 )
Using SQL to reduce the RAM usage. (0d8310d , 1006535 , e3fecc5 , 807da21 )
Delete min_precursor_mass and max_precursor_mass parameters. Delete a unnecessary filter. (b7ef385 )
Fixed Bugs:
Fix a bug caused by failing to get the host name. (0c60e56 )
Fix a bug that MS level checking is only needed in mzXML format. (72ffd87 )
Fix a bug that caused by empty spectrum. (c5325af , a3262e0 )
Fix a bug when there is no results in estimating FDR. (63deabe , d368f5e )
Fix a serious bug in CalEValue and improve CalEValue a lot. (418d314 , ff49e7e )
Fix a serious bug that may not check the middle bins' combinations. (a4cc349 )
Fix a bug in C-C setting. (8398aa4 )
Fix a serious bug that does not include any variable modification. (5325db3 )
Minor Changes:
Update some library versions and minor improve pom. (449fbff )
Change some default values in the paremeter.def. (60b2d30 )
Using ProteomicsLibrary's methods. (c100de8 , c3c6c20 , 6b88a18 , 9442bb5 )
Sort the PSMs according to their scores. (382b53a )
Improve the procedure of generating theoretical fragment ions and calculating XCorr. (a212c13 )
Delete a debug output. (82cd63f )
Improvement. Assume all advanced parameters are in the parameter.def. Delete unnecessary trim(). (3209614 )
Improve logger output. (4c3b840 )
Add more explanation to the parameter file. (4ca9035 )
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