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Revision 1326 - Directory Listing
Modified Thu Mar 3 13:21:18 2011 UTC (10 years, 3 months ago) by jmduarteg
Renamed xxxxError classes to xxxxException as they should be.
Revision 1306 - Directory Listing
Modified Tue Jan 25 14:15:20 2011 UTC (10 years, 4 months ago) by jmduarteg
Added Serializable interface to many classes. To be able to serialize classes containing objects of these types.
Revision 1305 - Directory Listing
Modified Fri Jan 21 10:11:16 2011 UTC (10 years, 5 months ago) by jmduarteg
Renaming all xxxxError named exceptions to xxxxException. Long overdue thing (was historical because it came from python). Learnt just recently that java does have a concept of Error too.
Revision 1166 - Directory Listing
Modified Fri Jul 30 14:58:26 2010 UTC (10 years, 10 months ago) by jmduarteg
Fixed bug: not allowing anymore the presence of gaps when choosing the representative CDS to uniprot match. Now the nucleotide alignments should be always correct (before they were shifted if there were gaps in CDS-to-uniprot)
Revision 1147 - Directory Listing
Modified Mon Jul 5 08:35:15 2010 UTC (10 years, 11 months ago) by jmduarteg
Implemented logging with log4j library
Revision 1143 - Directory Listing
Modified Thu Jul 1 10:02:53 2010 UTC (10 years, 11 months ago) by jmduarteg
New methods to check for reliability of positions with respect of the CDS matching
Revision 1140 - Directory Listing
Modified Tue Jun 29 08:49:34 2010 UTC (10 years, 11 months ago) by jmduarteg
Fixed bug: now nucleotide alignment is in same order as protein alignment
Revision 1116 - Directory Listing
Modified Thu Jun 17 09:48:22 2010 UTC (11 years ago) by jmduarteg
Now properly translating all frames and finding the best translation match in checkEmblCDSMatching. New class doing all the matching of protein to CDS.
Revision 1095 - Directory Listing
Modified Wed Jun 2 15:06:46 2010 UTC (11 years ago) by jmduarteg
Fixed bug: was nullpointing when the letter encountered in counting the column was unknown.
Revision 1094 - Directory Listing
Modified Wed Jun 2 13:19:21 2010 UTC (11 years ago) by jmduarteg
Implemented reduced alphabets in AminoAcid class and modified entropy calculation to allow reduced alphabets.
Revision 1074 - Directory Listing
Modified Fri May 21 10:02:24 2010 UTC (11 years, 1 month ago) by jmduarteg
Implemented profile counting and entropy calculation for alignment.
Revision 1072 - Directory Listing
Modified Thu May 20 13:59:25 2010 UTC (11 years, 1 month ago) by jmduarteg
Implemented methods to run a tcoffee alignment. Now also retrieving uniprot sequences via the uniprot api.
Revision 1054 - Directory Listing
Modified Wed Apr 28 13:37:00 2010 UTC (11 years, 1 month ago) by jmduarteg
Minor changes, couple of new methods.
Revision 1051 - Directory Listing
Modified Tue Apr 27 15:34:38 2010 UTC (11 years, 1 month ago) by jmduarteg
Minor fix to java docs
Revision 1027 - Directory Listing
Modified Fri Apr 16 10:03:57 2010 UTC (11 years, 2 months ago) by jmduarteg
Fixed some docs and indentation
Revision 1010 - Directory Listing
Modified Wed Mar 31 16:05:52 2010 UTC (11 years, 2 months ago) by hstehr
refactoring: removed a warning in MultipleSequenceAlignment and deleted obsolete directory src/tests
Revision 1009 - Directory Listing
Added Wed Mar 31 15:50:04 2010 UTC (11 years, 2 months ago) by hstehr
refactoring: moved many many classes to more appropriate packages; created new packages owl.core.sequence.alignment, owl.core.structure.alignment, owl.core.structure.features