Revision 492 - (view) (annotate) - [select for diffs]
Modified Wed Jan 2 13:18:57 2008 UTC (16 years, 9 months ago) by duarte
File length: 1001 byte(s)
Diff to previous 419

Copied the aglappe-jung branch into trunk.

Revision 419 - (view) (annotate) - [select for diffs]
Modified Thu Nov 22 14:09:18 2007 UTC (16 years, 11 months ago) by duarte
Original Path: branches/aglappe-jung/proteinstructure/GraphFileFormatError.java
File length: 1001 byte(s)
Diff to previous 385

Re-branching for JUNG2 development

Revision 385 - (view) (annotate) - [select for diffs]
Modified Wed Nov 7 17:32:43 2007 UTC (16 years, 11 months ago) by lpetzo
File length: 1001 byte(s)
Diff to previous 208

NEW TYPES
---------
- FileFormatError
- FastaFileFormatError
- PirFileFormatError
- AlignmentConstructionError

MODIFICATIONS
-------------
class Alignment:
- introduced new exceptions to be throw whenever file format error have been detected or any other construction errors occur
- changed accession rules of function getGapCharacter from "public" to "public static"
- new functions:
 * writeFasta
 
class CiffileFormatError:
- changed super class from Exception to the new FileFormatError class

class GraphFileFormatError:
- s. class CiffileFormatError

class PairwiseAlignmentConverter:
- added exception handling features due to class Alignment

class PairwiseAlignmentGraphConverter:
- s. class PairwiseAlignmentConverter

class PdbFileFormatError:
- s. class CifffileFormatError

Revision 208 - (view) (annotate) - [select for diffs]
Added Wed Jun 27 14:42:12 2007 UTC (17 years, 3 months ago) by duarte
File length: 480 byte(s)

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