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r1704
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jars/ 1647 (3 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.
modelit/ 1301 (5 years ago) by hstehr: overwriting default contactTypes.dat with the one needed for CMView release versions (only contains standard contact types). The old version with all esoteric contact types is renamed to contactTypes.all.dat
reconstruct/ 992 (6 years ago) by jmduarteg: Removed unneeded code
scripts/ 1633 (3 years ago) by jmduarteg: Removing uniprot update script, doesn't belong in owl repo
src/ 1704 (2 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.
.classpath 1647 (3 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.
.project 1638 (3 years ago) by jmduarteg: Changing default eclipse project name to owl
LICENSE 974 (6 years ago) by duarte: Adding license files
build.xml 1644 (3 years ago) by kumaran: 1)Javaversion variable is added in build.xml to change the version easily. 2)Pymol exited with error status 139 due to very long selection string written in the form of every residue(3+4+5+8+9+10). It is fixed by writing in the form of (3-5+8-10)
gpl.txt 974 (6 years ago) by duarte: Adding license files
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svn:ignore .classpath .project .settings build