Revision 1372 - (view) (annotate) - [select for diffs]
Modified Wed Mar 30 09:55:49 2011 UTC (13 years, 6 months ago) by jmduarteg
File length: 1357 byte(s)
Diff to previous 1009

MAJOR INTERFACE CHANGE: the main PDB data loading interface has changed. Now all loading of data occurs through PdbAsymUnit. Refactoring of some classes: Pdb is now PdbChain.

Revision 1009 - (view) (annotate) - [select for diffs]
Modified Wed Mar 31 15:50:04 2010 UTC (14 years, 6 months ago) by hstehr
File length: 1181 byte(s)
Diff to previous 1005

refactoring: moved many many classes to more appropriate packages; created new packages owl.core.sequence.alignment, owl.core.structure.alignment, owl.core.structure.features

Revision 1005 - (view) (annotate) - [select for diffs]
Modified Wed Mar 31 12:29:26 2010 UTC (14 years, 6 months ago) by hstehr
File length: 1139 byte(s)
Diff to previous 953

refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core

Revision 953 - (view) (annotate) - [select for diffs]
Modified Mon Feb 8 15:36:45 2010 UTC (14 years, 7 months ago) by duarte
File length: 1136 byte(s)
Diff to previous 951

Refactoring of inconsistently named methods in RIGraph

Revision 951 - (view) (annotate) - [select for diffs]
Modified Fri Jan 29 16:12:34 2010 UTC (14 years, 8 months ago) by duarte
File length: 1160 byte(s)
Copied from: trunk/compareCMs.java revision 950
Diff to previous 950

Reorganised the project with a src folder for java source files.
Added a jars dir with all jars needed for the project.
Added .project and .classpath pointing to relative path of jars. 
The project should now work out of the box after a check-out with eclipse. No need to setup external jars or anything.

Revision 950 - (view) (annotate) - [select for diffs]
Modified Fri Jan 29 11:57:38 2010 UTC (14 years, 8 months ago) by duarte
Original Path: trunk/compareCMs.java
File length: 1160 byte(s)
Diff to previous 492

Major refactoring and clean-up.
Most important changes are some methods in Pdb class: get_graph->getRIGraph and dump2pdb->writeToPDBFile
Removed all specific FileFormatError exception classes, now using only the generic FileFormatError.
All tests passed.

Revision 492 - (view) (annotate) - [select for diffs]
Modified Wed Jan 2 13:18:57 2008 UTC (16 years, 8 months ago) by duarte
Original Path: trunk/compareCMs.java
File length: 1158 byte(s)
Copied from: branches/aglappe-jung/compareCMs.java revision 491
Diff to previous 441

Copied the aglappe-jung branch into trunk.

Revision 441 - (view) (annotate) - [select for diffs]
Modified Thu Nov 29 15:19:37 2007 UTC (16 years, 10 months ago) by duarte
Original Path: branches/aglappe-jung/compareCMs.java
File length: 1158 byte(s)
Diff to previous 423

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)

Revision 423 - (view) (annotate) - [select for diffs]
Modified Fri Nov 23 13:37:17 2007 UTC (16 years, 10 months ago) by duarte
Original Path: branches/aglappe-jung/compareCMs.java
File length: 1285 byte(s)
Diff to previous 419

New methods in RIGraph copy() and compare(other)
Basic testing of copy introduced on testJUNGframework

Revision 419 - (view) (annotate) - [select for diffs]
Modified Thu Nov 22 14:09:18 2007 UTC (16 years, 10 months ago) by duarte
Original Path: branches/aglappe-jung/compareCMs.java
File length: 1273 byte(s)
Diff to previous 215

Re-branching for JUNG2 development

Revision 215 - (view) (annotate) - [select for diffs]
Modified Thu Jun 28 15:43:04 2007 UTC (17 years, 3 months ago) by stehr
Original Path: trunk/compareCMs.java
File length: 1273 byte(s)
Diff to previous 207

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 207 - (view) (annotate) - [select for diffs]
Modified Wed Jun 27 11:06:34 2007 UTC (17 years, 3 months ago) by duarte
Original Path: trunk/compareCMs.java
File length: 1277 byte(s)
Diff to previous 189

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 189 - (view) (annotate) - [select for diffs]
Added Tue Jun 12 10:38:29 2007 UTC (17 years, 3 months ago) by duarte
Original Path: trunk/compareCMs.java
File length: 1603 byte(s)

Added basic compare method to the Graph class and test class compareCMs