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r1070
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util/ 1042 (11 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)
features/ 1049 (11 years ago) by hstehr: removing @Override annotations which were causing compilation errors for me
connections/ 1062 (11 years ago) by stehr: fixed a minor bug in JPredConnection; new method SecondaryStructure.getConsensusSecondaryStructure(); changed visibility of RIGEnsemble.addFile() to public
structure/ 1067 (11 years ago) by hstehr: fixed a bug in SecondaryStructure.print(); added SecStrucElement.toString()
sequence/ 1069 (11 years ago) by jmduarteg: New methods to retrieve uniprot data and embl cds for a single homolog
runners/ 1070 (11 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.
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