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Tagging for eppic release 2.0.3 - more PDB metadata parsing: biounit assembly and release date - improved rmsd calculation: new OptimalSuperposition class introduced - improvements in interface calculation: now going to 12th cell - introduced chain clusters and interface clusters - some more checks in cif file parsing: now won't crash on phenix files
Fixing bug in jaligner: the NeedlemanWunschGotoh method used by owl.core.sequence.PairwiseSequenceAlignment had a bug causing infinite hanging when using very long sequences. The issue would happen when either of the 2 sequences to align was longer than 32768 (16 bit) and the other sequence would match it after the 32768 region, a test case is included in this commit to demonstrate it. The problem was an overflow: an array used for the traceback procedure was declared as short[] (16 bit), changing it to int[] (32 bit) the issue disappears. As the development in jaligner seems to be stopped I've simply downloaded the source, fixed the issue there (plus removing the loggers) and repackaged in a jar (jaligner-bugfixed.jar) that includes the sources.
Removing unused class and thus JRclient dependency
Updated uniprot japi jars
Updating common-maths jar to latest stable release 2.2 (from 1.2)
preparing for adding 'mutanom' package: adding dependencies to jars dir
Control database access! for CGAP
reverting changes to .project and .classpath which were accidentally committed
fixed a bug in GraphAverager.getGraphWithTopContacts() which caused a null pointer exception in jung.SparseGraph.addEdge(), this may even be a bug in jung
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.
Updated jung jars to version 2.0.1 (finally the release version, not alpha or beta!)
Reorganised the project with a src folder for java source files. Added a jars dir with all jars needed for the project. Added .project and .classpath pointing to relative path of jars. The project should now work out of the box after a check-out with eclipse. No need to setup external jars or anything.
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