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root/owl/trunk/src/owl/core/runners/blast
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Revision 1326 - Directory Listing
Modified Thu Mar 3 13:21:18 2011 UTC (10 years, 10 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 (11 years 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 (11 years 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 1304 - Directory Listing
Modified Sun Jan 16 16:06:09 2011 UTC (11 years ago) by jmduarteg
Fixed important bug: we didn't model the blast data properly. A hit is composed of several hsps. Now our classes following that data model properly (before we treated a hit as an hsp).
Revision 1106 - Directory Listing
Modified Thu Jun 10 09:24:30 2010 UTC (11 years, 7 months ago) by jmduarteg
Implemented caching of blast in UniprotHomologList
Revision 1045 - Directory Listing
Modified Mon Apr 26 12:55:28 2010 UTC (11 years, 9 months ago) by jmduarteg
Uniprot and embl ws dbfetch connections can now do multiple entries per request. Update to parse also the hit_def tag in blast parser.
Revision 1043 - Directory Listing
Modified Thu Apr 22 12:21:37 2010 UTC (11 years, 9 months ago) by jmduarteg
Fixed blast parsing bug: was parsing the Hit_def tag instead of the Hit_id tag for the subject id. When formatdb is run with option "-o T" then indices are properly generated and Hit_id contains the correct tag.
Revision 1009 - Directory Listing
Modified Wed Mar 31 15:50:04 2010 UTC (11 years, 9 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
Revision 1006 - Directory Listing
Added Wed Mar 31 13:00:35 2010 UTC (11 years, 9 months ago) by hstehr
refactoring: created packages runners.blast, runners.gromacs, structure.graphs, moved actionTools to util, structure.decoyScoring to owl.decoyScoring, tinker to runners.tinker