ECL2-2.1.9

This is a minor upgrade to fix some security vulnerabilities in some libraries

1. Upgrade JUnit to 1.13.2 due to the security vulnerabilities.
2. Upgrade Logback to 1.2.8 due to the security vulnerabilities.
3. Upgrade Guava to 31.0.1 due to the security vulnerabilities.
4. Upgrade sqlite-jdbc to 3.36.0.2.

ECL2-2.1.8

Major changes

1. Delete q-value column in the decoy output to avoid the confusion. (40d33b2)
2. Support more enzymes. (58b5a76)
3. Support up to two enzymes simultaneously. (62947bb)
4. Using "Others" as the default database type to make sure that there won't be any error if the database type is incorrect. (8864a64)

Minor changes

1. Improve ProGuard parameters.
2. Fix bugs.
3. Minor improvements.
4. Optimize logger outputs.
5. Update some libraries to the latest version.

2.1.8-79b912

Major changes:

1. 79b9123@Fall back to the linear FDR estimation approach when fuse_count < decoy_count. This change will affect the results a lot in some cases.
2. 58b5a76@Support more enzymes.
3. 62947bb@Support up to two enzymes simultaneously.
4. af07e84@Add running time to logger and minor improvement.
5. 40d33b2@Delete q-value column in the decoy output to avoid a confusion.
6. 3c8f9fd@One more database_type in the parameter.
7. c4f5bd0@Output some warnings regarding the "not enough data points" issue.

Minor changes:

Fix bugs and add small improvements.

ECL2-2.1.7

Add a link_same_peptide option.

ECL2-2.1.6

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)

ECL2-2.1.5

Bug fix:

1. Fix a bug due to different locale format. (50fd06f)
2. FIx a bug that doesn't record multiple proteins for one sequence. (a8f0947)

Improvement:

1. Update packages and pom information. (433b183, 9ea1966)
2. Improve MGF title parse and error output. (145eb70)

ECL2-2.1.4

Big improvements

1. Add binary var mod. (a32411c)
2. Support new cross-linkers. (bbf133d)
3. Output raw spectrum, normalized spectrum, xcorr spectrum, and two chains' theoretical spectra in debug mode. (a133aee)
4. Finding the start and end points in e-value estimation based on Comet. (c527973)
5. Improve the preprocessing part. (add5476)
6. Add flanking peak as an option. (a4ef245, 840dfd4)
7. Improve the dot() function. (659819a)
8. Eliminate the uniprot decoy pool. (588ccda)
9. Improve e-value estimation. (538a031)
10. Eliminate "min_peak_num" parameter. (20d7186)
11. Add a "single_chain_t" parameter. (4fb5646)
12. Add "cal_evalue" as an option. (8e6d5d5)
13. Add some advanced parameters. (e6b5baf)
14. Add a parameter file version. (1c9b46a)
15. Add "delta_c_t" as an option. (91b4444)
16. Add computer's name. (54ff9fd)
17. A big improvement in generating the random histogram. (c0b0b40)
18. Add initialCapacity and loadFactor. (60db667)
19. Improve the search part. (46c487a)

Many bug fix and improvements

Please check the comments.

ECL2.0-2.1.3

New release.