Revision 215 - (view) (annotate) - [select for diffs]
Modified Thu Jun 28 15:43:04 2007 UTC (17 years, 8 months ago) by stehr
File length: 2429 byte(s)
Diff to previous 208

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 208 - (view) (annotate) - [select for diffs]
Modified Wed Jun 27 14:42:12 2007 UTC (17 years, 8 months ago) by duarte
File length: 2433 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]
Modified Wed Jun 27 11:06:34 2007 UTC (17 years, 8 months ago) by duarte
File length: 2411 byte(s)
Diff to previous 206

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

Revision 206 - (view) (annotate) - [select for diffs]
Modified Tue Jun 26 17:01:48 2007 UTC (17 years, 8 months ago) by duarte
File length: 2264 byte(s)
Diff to previous 202

Major refactoring:
 accode -> pdbCode
 chaincode -> pdbChainCode
 chain -> chainCode
Major change of signatures (publics to privates)
Implemented getters for needed member variables
Major clean up

Revision 202 - (view) (annotate) - [select for diffs]
Modified Thu Jun 21 17:18:11 2007 UTC (17 years, 8 months ago) by duarte
File length: 2255 byte(s)
Diff to previous 162

MySQLConnection now throwing SQLException on connect
Many files changed following this: all calling classes now re-throwing or catching the SQLException

Revision 162 - (view) (annotate) - [select for diffs]
Modified Thu May 24 10:46:39 2007 UTC (17 years, 9 months ago) by duarte
File length: 2181 byte(s)
Diff to previous 132

Updated test class for Pdb/Graph objects

Revision 132 - (view) (annotate) - [select for diffs]
Modified Thu May 10 16:04:06 2007 UTC (17 years, 9 months ago) by duarte
File length: 2366 byte(s)
Diff to previous 127

Added more tests for all cases

Revision 127 - (view) (annotate) - [select for diffs]
Modified Wed May 9 14:54:02 2007 UTC (17 years, 9 months ago) by duarte
File length: 1130 byte(s)
Diff to previous 125

Implemented read of pdb data from pdb file.
FIXED BUG in dumping of pdb file. Was missing end of line in atom lines
Added more tests in testPdb

Revision 125 - (view) (annotate) - [select for diffs]
Added Wed May 9 11:58:59 2007 UTC (17 years, 9 months ago) by duarte
File length: 769 byte(s)

Initial commit of testPdb, to test the proteinstructure package