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r1324
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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
graphAveraging/ 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.
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.
casp/ 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.
gmbp/ 1316 (8 years ago) by jmduarteg: Got rid (finally!) of AAinfo. Its functionality is now in ContactType and AminoAcid.
embed/ 1316 (8 years ago) by jmduarteg: Got rid (finally!) of AAinfo. Its functionality is now in ContactType and AminoAcid.
decoyScoring/ 1316 (8 years ago) by jmduarteg: Got rid (finally!) of AAinfo. Its functionality is now in ContactType and AminoAcid.
core/ 1324 (8 years ago) by jmduarteg: A few bug fixes and improvements in pdb data parsing. - bug fix: in some cases exptl method field has more than 1 value (e.g. 2krl). In cif files this was causing a null pointer. We now parse it properly (taking first one as the exptl method) in both cif and pdb files - improved very slightly the cif file parser moving out of loops the index getters - drop fullLength as a field in Pdb, now we have only getFullLength() - pdb file atom parsing is now column based and not regex based (hopefully will make it slightly faster) - now parsing the element column of pdb files: now the atom type detection comes from the appropriate field in pdb/cif/pdbase. If in pdb file and not present we still try to guess it as before
tests/ 1324 (8 years ago) by jmduarteg: A few bug fixes and improvements in pdb data parsing. - bug fix: in some cases exptl method field has more than 1 value (e.g. 2krl). In cif files this was causing a null pointer. We now parse it properly (taking first one as the exptl method) in both cif and pdb files - improved very slightly the cif file parser moving out of loops the index getters - drop fullLength as a field in Pdb, now we have only getFullLength() - pdb file atom parsing is now column based and not regex based (hopefully will make it slightly faster) - now parsing the element column of pdb files: now the atom type detection comes from the appropriate field in pdb/cif/pdbase. If in pdb file and not present we still try to guess it as before
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