Revision 1166 - Directory Listing
Modified Fri Jul 30 14:58:26 2010 UTC (12 years 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 (12 years, 1 month ago) by jmduarteg

Implemented logging with log4j library

Revision 1143 - Directory Listing
Modified Thu Jul 1 10:02:53 2010 UTC (12 years, 1 month 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 (12 years, 1 month 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 (12 years, 1 month 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 (12 years, 2 months 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 (12 years, 2 months 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 (12 years, 2 months ago) by jmduarteg

Implemented profile counting and entropy calculation for alignment.

Revision 1072 - Directory Listing
Modified Thu May 20 13:59:25 2010 UTC (12 years, 2 months 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 (12 years, 3 months ago) by jmduarteg

Minor changes, couple of new methods.

Revision 1051 - Directory Listing
Modified Tue Apr 27 15:34:38 2010 UTC (12 years, 3 months ago) by jmduarteg

Minor fix to java docs

Revision 1027 - Directory Listing
Modified Fri Apr 16 10:03:57 2010 UTC (12 years, 3 months ago) by jmduarteg

Fixed some docs and indentation

Revision 1010 - Directory Listing
Modified Wed Mar 31 16:05:52 2010 UTC (12 years, 4 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 (12 years, 4 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