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r1704
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connections/ 1372 (10 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.
sequence/ 1647 (8 years ago) by jmduarteg: 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.
util/ 1657 (8 years ago) by jmduarteg: Removed many warnings (appearing thanks to better checking in eclipse 4.3)
runners/ 1698 (7 years ago) by jmduarteg: Important change: removed PDBASE support. The PDBASE database is difficult to create plus there's no support for it whatsover, additionally the code was already obsolete for PDBASE reading. Now all instances of PDBASE loading have been converted to mmCIF file loading. Additionally: massive clean-up of obsolete classes.
structure/ 1704 (7 years ago) by jmduarteg: Fixed bug in cif file parsing: was not tokenising correctly loop elements that had more multi-line quoting mixed with normal quoted fields and several records. Added one more test case for that.
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