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r1647
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litNet/ 1007 (9 years ago) by hstehr: refactoring: moved casp, deltaRank, embed, graphAveraging, ppi, sadp to owl
ppi/ 1007 (9 years ago) by hstehr: refactoring: moved casp, deltaRank, embed, graphAveraging, ppi, sadp to owl
sadp/ 1305 (8 years ago) by jmduarteg: Renaming all xxxxError named exceptions to xxxxException. Long overdue thing (was historical because it came from python). Learnt just recently that java does have a concept of Error too.
deltaRank/ 1314 (8 years ago) by jmduarteg: Finally got rid of all duplicated amino acid methods in AAinfo. Now everything unified in AminoAcid enum.
graphAveraging/ 1392 (8 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.
gmbp/ 1392 (8 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.
mutanom/ 1392 (8 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.
decoyScoring/ 1392 (8 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.
cccp/ 1399 (8 years ago) by jmduarteg: Improved PDB file writing: now writing SEQRES lines and fixed some formatting issues with long atom names (i.e. CL, NA,...)
embed/ 1399 (8 years ago) by jmduarteg: Improved PDB file writing: now writing SEQRES lines and fixed some formatting issues with long atom names (i.e. CL, NA,...)
casp/ 1597 (6 years ago) by jmduarteg: Several changes related to blast: - now supporting blast+ blastp. - blast xml parser can now ignore the DTD url, avoiding unnecessary network access if desired - refactoring: legacy blast related stuff is now refactored to contain "legacy", runBlastp refers to blast+ Also updated uniprot jar.
core/ 1646 (6 years ago) by jmduarteg: Now interfaces pngs have transparent background. Also changed another instance of "select resi 0" to "select none"
tests/ 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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