ViewVC Help
View Directory | Revision Log | Download Tarball | View Changeset | Root Listing
root/owl/trunk/src/owl/core/connections
r1324
File Last Change
 ../
pisa/ 1312 (10 years ago) by jmduarteg: Put back the parsing of score p values (was commented out)
CSAConnection.java 1324 (10 years ago) by jmduarteg: A few bug fixes and improvements in pdb data parsing. - bug fix: in some cases exptl method field has more than 1 value (e.g. 2krl). In cif files this was causing a null pointer. We now parse it properly (taking first one as the exptl method) in both cif and pdb files - improved very slightly the cif file parser moving out of loops the index getters - drop fullLength as a field in Pdb, now we have only getFullLength() - pdb file atom parsing is now column based and not regex based (hopefully will make it slightly faster) - now parsing the element column of pdb files: now the atom type detection comes from the appropriate field in pdb/cif/pdbase. If in pdb file and not present we still try to guess it as before
ConsurfConnection.java 1005 (11 years ago) by hstehr: refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
ECConnection.java 1035 (11 years ago) by jmduarteg: Extracted the EC data parsing code to its own connection class.
EmblWSDBfetchConnection.java 1266 (10 years ago) by jmduarteg: Now throwing IOException when the server returns an error (happens for example when it is down)
GTGHit.java 1305 (10 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.
GTGHitList.java 1305 (10 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.
GTGParser.java 1305 (10 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.
JPredConnection.java 1062 (11 years ago) by stehr: fixed a minor bug in JPredConnection; new method SecondaryStructure.getConsensusSecondaryStructure(); changed visibility of RIGEnsemble.addFile() to public
JPredProgressRetriever.java 1060 (11 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.
JPredStopNotifier.java 1060 (11 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.
NoMatchFoundException.java 1040 (11 years 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.
PDomainsConnection.java 1005 (11 years ago) by hstehr: refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
PhosphoSiteConnection.java 1231 (10 years ago) by hstehr: Adding class PhosphoSiteConnection
PrositeHit.java 1009 (11 years 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
PrositeScanner.java 1009 (11 years 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
ScopConnection.java 1034 (11 years ago) by jmduarteg: Extracted Scop parsing code to its own connection class.
SiftsConnection.java 1226 (10 years ago) by hstehr: Refactoring of SiftsConnection and SiftsFeature, now implementing Uniprot2Pdb
UniProtConnection.java 1310 (10 years ago) by jmduarteg: Fixed bug: was not checking whether the uniprot japi was actually returning all requested records for ids given when using getMultipleEntries. Now checking, logging it and removing the not-found ids from the homolog list.
UniProtPdbRef.java 1234 (10 years ago) by hstehr: New method to get PDB cross refs for a Uniprot entry
package-info.java 1005 (11 years ago) by hstehr: refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
         20 files shown