Revision 234 - (view) (annotate) - [select for diffs]
Modified Tue Jul 10 14:14:58 2007 UTC (17 years, 2 months ago) by duarte
File length: 10140 byte(s)
Diff to previous 217

Made ContactList a TreeSet instead of an ArrayList, should improve performance (log(n) rather than linear)
REFACTORING: 
ContactList -> EdgeSet
Contact -> Edge

Revision 217 - (view) (annotate) - [select for diffs]
Modified Fri Jun 29 09:04:00 2007 UTC (17 years, 3 months ago) by stehr
File length: 10147 byte(s)
Diff to previous 215

now casting pdb codes to lower and pdb chain codes to upper in all constructors

Revision 215 - (view) (annotate) - [select for diffs]
Modified Thu Jun 28 15:43:04 2007 UTC (17 years, 3 months ago) by stehr
File length: 10026 byte(s)
Diff to previous 210

some clean up of exceptions in Pdb and Graph classes:
merged PdbAcCodeNotFoundError and MsdAcCodeNotFoundError into PdbCodeNotFoundError,
created new PdbChainCodeNotFound, got rid of stderr output, throwing exceptions with informative messages instead

Revision 210 - (view) (annotate) - [select for diffs]
Modified Wed Jun 27 15:57:39 2007 UTC (17 years, 3 months ago) by duarte
File length: 10022 byte(s)
Diff to previous 208

Now throwing also SQLExceptions for individual queries, not just for connections

Revision 208 - (view) (annotate) - [select for diffs]
Modified Wed Jun 27 14:42:12 2007 UTC (17 years, 3 months ago) by duarte
File length: 10096 byte(s)
Diff to previous 207

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

Revision 207 - (view) (annotate) - [select for diffs]
Added Wed Jun 27 11:06:34 2007 UTC (17 years, 3 months ago) by duarte
File length: 9820 byte(s)

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