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Made ContactList a TreeSet instead of an ArrayList, should improve performance (log(n) rather than linear) REFACTORING: ContactList -> EdgeSet Contact -> Edge
Fixed bug in regex introduced in last revision
Fixed graph file format checking, was not working properly
Throwing exception also in case graph file not in right format at all (no #AGLAPPE in 1st line) Fixed bug: was not reading correctly #PDB CHAIN CODE
FIXED BUGS: - directed was not set when reading from cm file - pdbChainCode not set when reading from db given pdbCode - filling pdbresser2resser and resser2pdbresser hashmaps also in reading from pdb file - using "A" as chainCode when reading from pdb file - some error handling for file formats: new exception classes GraphFileFormatError and PdbfileFormatError
Restructured construction of Pdb and Graph objects: now subclasses for each case Cleaned up and made consistent database connections Now can also pass a MySQLConnection in all cases (as well as having default values for a default connection) PdbaseInfo and MsdsdInfo classes removed: now merged into PdbasePdb and MsdsdPdb respectively Updated following this changes testPdb and compareCMs
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