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Revision 1597 - Directory Listing
Modified Wed Nov 7 08:58:43 2012 UTC (9 years, 1 month ago) by jmduarteg
Several changes related to blast:
- now supporting blast+ blastp. 
- blast xml parser can now ignore the DTD url, avoiding unnecessary network access if desired
- refactoring: legacy blast related stuff is now refactored to contain "legacy", runBlastp refers to blast+
Also updated uniprot jar.
Revision 1491 - Directory Listing
Modified Thu Nov 17 14:56:11 2011 UTC (10 years ago) by jmduarteg
Now can pass option -v to blast (max number of hits reported)
Revision 1392 - Directory Listing
Modified Thu May 19 14:27:50 2011 UTC (10 years, 6 months ago) by jmduarteg
MAJOR CHANGE: now able to read and treat properly HETATMS and nucleotides from PDB entries. All tests pass. Anyway surely there will be some bugs to iron out still.
Revision 1372 - Directory Listing
Modified Wed Mar 30 09:55:49 2011 UTC (10 years, 8 months ago) by jmduarteg
MAJOR INTERFACE CHANGE: the main PDB data loading interface has changed. Now all loading of data occurs through PdbAsymUnit. Refactoring of some classes: Pdb is now PdbChain.
Revision 1341 - Directory Listing
Modified Tue Mar 15 08:40:43 2011 UTC (10 years, 8 months ago) by jmduarteg
Now parsing pdb titles in PDB, CIF and pdbase. Tests pass.
Moved some constants from Pdb to PdbAsymUnit
Revision 1326 - Directory Listing
Modified Thu Mar 3 13:21:18 2011 UTC (10 years, 9 months ago) by jmduarteg
Renamed xxxxError classes to xxxxException as they should be.
Revision 1313 - Directory Listing
Modified Wed Feb 9 10:28:56 2011 UTC (10 years, 10 months ago) by jmduarteg
Now taking paths from owl_test_paths.dat file
Revision 1305 - Directory Listing
Modified Fri Jan 21 10:11:16 2011 UTC (10 years, 10 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 1304 - Directory Listing
Modified Sun Jan 16 16:06:09 2011 UTC (10 years, 10 months 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 1030 - Directory Listing
Modified Mon Apr 19 09:39:07 2010 UTC (11 years, 7 months ago) by jmduarteg
Extracted constants to owl_test_paths.dat and added CASP7 fasta files to resources dir. Now BlastParsersTest should be able to run anywhere.
Revision 1009 - Directory Listing
Modified Wed Mar 31 15:50:04 2010 UTC (11 years, 8 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 1008 - Directory Listing
Added Wed Mar 31 14:03:27 2010 UTC (11 years, 8 months ago) by hstehr
refactoring: adapting test packages to match new package structure