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Revision 1597 - Directory Listing
Modified Wed Nov 7 08:58:43 2012 UTC (8 years, 10 months 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 (9 years, 10 months 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, 4 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, 5 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, 6 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, 6 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, 7 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, 7 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, 8 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, 5 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, 5 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, 5 months ago) by hstehr
refactoring: adapting test packages to match new package structure