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Extracted constant NULL_CHAIN_CODE that was still hard-coded in MANY places. Now should be safe to replace the value of the constant from "NULL" to something else. Using TemplateList.readIdsListFile() in averageGraph, dumpseq and genGraph so that is now a standard way of reading list files with pdbcodes/chaincodes. NOTE: this introduces an incompatibility with legacy list files: we can't read a NULL pdb chain code with the "NULL" string e.g. '1i1b NULL'. This is fine because since PDB-REMEDIATED all NULL chains are now "A". Fixed a few things and made more standard the scripts dumpseq and genGraph
Not reporting time anymore in genGraph Fixed again the help text
New switch -P to write file in paul format instead of aglappe format
Copied the aglappe-jung branch into trunk.
Now Pdb constructors don't load data but rather intialise the pdbCode, loading occurs upon call of load(pdbChainCode,modelSerial) New methods getChains() and getModels() in all Pdb classes New Exception PdbLoadError New tester for getChains and getModels: testGetChains Changed all calls to Pdb construction accordingly (includes changing excpetions)
Fixed bug: was not working with crossed contacts (with "/") because the "/" was not allowed in file names. Now replacing / with :
Added last i/o method from old Graph (write to file in Ioannis network format) Using now the more correct degree, indegree, outdegree methods instead of count neighbor methods Fixed the write_graph_to_file method name in executables in default package
First implementation of the new graph framework using JUNG2. Still a few classes to fix, but all basic functionality is there. NOTE: at the moment ProtStructGraph is a SparseGraph which doesn't guarantee that the graph has no parallel or loop edges (I thought that would be solved by using the SimpleGraph interface but it doesn't, that's only a marker interface)
Re-branching for JUNG2 development
Added mode option in genDbGraph whether to find and store info for the residues (SCOP,NACCESS,EC,CSA,...)
Fixed a few bugs in reading of list file Better output and error messages
New script genGraph (generates graph to files) Better error messages in both
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