 ../
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pisa/
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1635
(9 years ago)
by jmduarteg:
Fixed pisa oligomeric prediction behaviour when mixed assembly sizes in same assembly group
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package-info.java
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1005
(12 years ago)
by hstehr:
refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
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UnirefXMLParser.java
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1557
(10 years ago)
by jmduarteg:
Fixed bug: for a uniref100 cluster member, was taking the representative's uniprot id/tax id instead of the member's. Database was not correctly modelled -> need also the tax ids for cluster members (and then to query the tax ids from members and not from representative)
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UniprotLocalConnection.java
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1642
(9 years ago)
by jmduarteg:
Now both taxonomy and uniprot tables are read from same database
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UniProtPdbRef.java
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1347
(11 years ago)
by hstehr:
moving project CCCP to this repository
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UniProtConnection.java
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1535
(10 years ago)
by jmduarteg:
Restructured how the UniprotConnection is used. Now all uniprot connection stuff done within the class
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SiftsConnection.java
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1637
(9 years ago)
by jmduarteg:
Minor javadoc improvement
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ScopConnection.java
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1472
(10 years ago)
by jmduarteg:
Fixed a couple of problems with ScopConnection. Added another atom type.
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PrositeScanner.java
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1009
(12 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
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PrositeHit.java
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1009
(12 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
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PiqsiConnection.java
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1598
(9 years ago)
by jmduarteg:
New classes to parse PiQSi annotation file
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PiqsiAnnotation.java
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1598
(9 years ago)
by jmduarteg:
New classes to parse PiQSi annotation file
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PhosphoSiteConnection.java
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1231
(11 years ago)
by hstehr:
Adding class PhosphoSiteConnection
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PDomainsConnection.java
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1347
(11 years ago)
by hstehr:
moving project CCCP to this repository
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NoMatchFoundException.java
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1040
(12 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.
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JPredStopNotifier.java
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1060
(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.
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JPredProgressRetriever.java
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1060
(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.
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JPredConnection.java
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1370
(11 years ago)
by hstehr:
Updated some JavaDocs
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GTGParser.java
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1326
(11 years ago)
by jmduarteg:
Renamed xxxxError classes to xxxxException as they should be.
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GTGHitList.java
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1326
(11 years ago)
by jmduarteg:
Renamed xxxxError classes to xxxxException as they should be.
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GTGHit.java
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1372
(11 years 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.
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EmblWSDBfetchConnection.java
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1507
(10 years ago)
by jmduarteg:
Now supporting both uniprot and uniparc entries in HomologList
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ECConnection.java
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1372
(11 years 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.
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CSAConnection.java
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1392
(11 years 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.
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