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r1647
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branches/ 1438 (8 years ago) by jmduarteg: An ant script for owl!
tags/ 1640 (6 years ago) by jmduarteg: Tagging for eppic release 2.0.1 - fixed bug: can't read 'I 1 2 1' space group. Now using both main and alternative names for looking up space groups
trunk/ 1647 (6 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.
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