Revision
1078 -
Directory Listing
Modified
Thu May 27 10:33:41 2010 UTC
(11 years, 11 months ago)
by
jmduarteg
Now parsing the seq_num residue number.
Revision
1077 -
Directory Listing
Modified
Thu May 27 09:51:50 2010 UTC
(11 years, 11 months ago)
by
jmduarteg
Fixed a bug in PISA xml parser: pdb code was upper case, need to convert to lower case.
Some new functionality in PISA classes
Revision
1075 -
Directory Listing
Modified
Fri May 21 17:33:34 2010 UTC
(12 years ago)
by
jmduarteg
PISA connection and xml interfaces description parser
Revision
1062 -
Directory Listing
Modified
Sun May 9 21:54:40 2010 UTC
(12 years ago)
by
stehr
fixed a minor bug in JPredConnection; new method SecondaryStructure.getConsensusSecondaryStructure(); changed visibility of RIGEnsemble.addFile() to public
Revision
1061 -
Directory Listing
Modified
Fri May 7 14:13:07 2010 UTC
(12 years ago)
by
hstehr
Adding the possibility to set the timeout for a JPredConnection. Next step is to add this as a user variable to CMView
Revision
1060 -
Directory Listing
Modified
Fri May 7 11:53:13 2010 UTC
(12 years ago)
by
hstehr
New helper classes JPredProgressRetriever and JPredNotifier which can be used to run JPredConnection in a thread and notify some GUI component of the progress.
Revision
1054 -
Directory Listing
Modified
Wed Apr 28 13:37:00 2010 UTC
(12 years ago)
by
jmduarteg
Minor changes, couple of new methods.
Revision
1052 -
Directory Listing
Modified
Tue Apr 27 16:07:48 2010 UTC
(12 years ago)
by
hstehr
Fixing bad bug in JPredConnection which would always load the results from my test example instead of the real one; some minor edits in RIGraph
Revision
1046 -
Directory Listing
Modified
Mon Apr 26 15:26:59 2010 UTC
(12 years ago)
by
hstehr
JPredConnection now returns a SecondaryStructure object; some updated javadocs
Revision
1045 -
Directory Listing
Modified
Mon Apr 26 12:55:28 2010 UTC
(12 years 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
1042 -
Directory Listing
Modified
Wed Apr 21 16:11:08 2010 UTC
(12 years, 1 month ago)
by
jmduarteg
New SiftsConnection and SiftsFeature classes for SIFTS pdb to uniprot mapping. Implemented the HasFeatures interface in Pdb. In the future we can hopefully use that mechanism for all features (sec. strucuture, scop and so on)
Revision
1041 -
Directory Listing
Modified
Wed Apr 21 13:24:18 2010 UTC
(12 years, 1 month ago)
by
hstehr
New class JPredConnection for querying the Barton group's JPred server for secondary structure-, burial- and coiled coil prediction. Minor updates of javadocs.
Revision
1040 -
Directory Listing
Modified
Wed Apr 21 10:44:19 2010 UTC
(12 years, 1 month ago)
by
jmduarteg
New UniprotConnection taken from Henning's structural impact project (lots of new jar dependencies with that). New EmblWSDBFetchConnection class to get sequences from EMBL web services.
Revision
1035 -
Directory Listing
Modified
Mon Apr 19 13:10:39 2010 UTC
(12 years, 1 month ago)
by
jmduarteg
Extracted the EC data parsing code to its own connection class.
Revision
1034 -
Directory Listing
Modified
Mon Apr 19 12:42:21 2010 UTC
(12 years, 1 month ago)
by
jmduarteg
Extracted Scop parsing code to its own connection class.
Revision
1033 -
Directory Listing
Modified
Mon Apr 19 12:26:22 2010 UTC
(12 years, 1 month ago)
by
jmduarteg
Extracted the CSA parsing code to its own connection class.
Revision
1009 -
Directory Listing
Modified
Wed Mar 31 15:50:04 2010 UTC
(12 years, 1 month 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
1005 -
Directory Listing
Modified
Wed Mar 31 12:29:26 2010 UTC
(12 years, 1 month ago)
by
hstehr
Copied from:
trunk/src/connections revision 1002
refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
Revision
987 -
Directory Listing
Modified
Thu Mar 18 11:08:58 2010 UTC
(12 years, 2 months ago)
by
jmduarteg
Original Path:
trunk/src/connections
New package runners for Runner classes. At the moment only contains the new class NaccessRunner (moved out of Pdb class)
Introduced a config file for tests so that one can set externally the executable paths and any other necessary data to run tests (at the moment only implemented in PdbTest.java). PdbTest now should run anywhere (if you have a local pdbase installation!)
Moved the consurf parser out of Pdb to its own class ConsurfConnection in the connection package.
Revision
985 -
Directory Listing
Added
Tue Mar 16 13:47:40 2010 UTC
(12 years, 2 months ago)
by
hstehr
Original Path:
trunk/src/connections
Adding new package owl.connections with connector classes to online databases and services. Starting with PhosphoSitePlusConnection for accessing a database of posttranslational modifications and PDomainsConnection for accessing a very useful webservice which calculates structural domains using a variety of methods including Scop, Cath, DomainParser, ProteinDomainParser and others.
