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File Last Change (rev)
core/ 1164 (11 years ago) by jmduarteg: Now returning null for the representative CDS when the gene encoding organelle is not nucleus/plasmid. Before the whole program would stop, which wasn't ideal. Eventually we will need to use the proper genetic code when needed.
gmbp/ 1163 (11 years ago) by jmduarteg: Got rid of german text (was causing a warning in compilation), anyway there shouldn't be any german... unless we start i8nsing.
sadp/ 1084 (11 years ago) by matt4077: renamed conflicting ContactMap class.
casp/ 1070 (12 years ago) by jmduarteg: Fixed bug in TcoffeeRunner. The t_coffee process was hanging after spawning. This didn't happen before, it can be related to the version of t_coffee (I'm using 8.14). Basically t_coffee seems to be doing something weird with stderr and stdout, java doesn't like it and makes the process hang (as usual java has a lot of problems in this area, see StreamGobbler class). The way to solve it is use the -quiet switch of t_coffee that can be used to redirect output to a file or have a complete quiet terminal.
graphAveraging/ 1066 (12 years ago) by hstehr: new methods needed for CCCP: RIGraph.addEdgeIJ(i,j,weight), RIGEnsembl.loadFromDirectory(), GraphAverager.addZeroEdges(), SecondaryStructure.print()
decoyScoring/ 1059 (12 years ago) by jmduarteg: Fixed java doc
deltaRank/ 1057 (12 years ago) by matt4077: add psi/phi constraints from secondary structure to tinker reconstructions
tests/ 1042 (12 years ago) by jmduarteg: New SiftsConnection and SiftsFeature classes for SIFTS pdb to uniprot mapping. Implemented the HasFeatures interface in Pdb. In the future we can hopefully use that mechanism for all features (sec. strucuture, scop and so on)
embed/ 1018 (12 years ago) by hstehr: removing a warning in owl.embed.contactmaps.Demes
litNet/ 1007 (12 years ago) by hstehr: refactoring: moved casp, deltaRank, embed, graphAveraging, ppi, sadp to owl
ppi/ 1007 (12 years ago) by hstehr: refactoring: moved casp, deltaRank, embed, graphAveraging, ppi, sadp to owl
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