Revision 326 - (view) (annotate) - [select for diffs]
Modified Thu Sep 20 14:49:55 2007 UTC (17 years ago) by duarte
File length: 2591 byte(s)
Diff to previous 281

Removed class AA and replace it by AAinfo, which reads contact types from separate file contactTypes.dat
New class ContactType which contains atoms for each contact type and residue. A static object for each contact type is loaded into AAinfo upon reading the contactTypes.dat file
Changed all references accordingly

Revision 281 - (view) (annotate) - [select for diffs]
Modified Tue Aug 14 13:49:52 2007 UTC (17 years, 1 month ago) by stehr
File length: 2579 byte(s)
Diff to previous 260

fixed little bug in NodeNbh

Revision 260 - (view) (annotate) - [select for diffs]
Modified Fri Aug 10 18:30:47 2007 UTC (17 years, 1 month ago) by duarte
File length: 2455 byte(s)
Diff to previous 233

Implemented write_graph_to_db
New member variable model in Graph, thus changed constructor
New methods to get degree of a node in Graph
New methos in NodeNbh to write other kinds of neighbourhood strings

Revision 233 - (view) (annotate) - [select for diffs]
Modified Tue Jul 10 13:01:50 2007 UTC (17 years, 2 months ago) by duarte
File length: 1889 byte(s)
Diff to previous 196

Added method getCopy

Revision 196 - (view) (annotate) - [select for diffs]
Modified Wed Jun 13 15:05:31 2007 UTC (17 years, 3 months ago) by duarte
File length: 1663 byte(s)
Diff to previous 193

Added toString and getMotifFullGaps missing in EdgeNbh

Revision 193 - (view) (annotate) - [select for diffs]
Modified Wed Jun 13 07:57:31 2007 UTC (17 years, 3 months ago) by duarte
File length: 1569 byte(s)
Diff to previous 186

Moved motif static methods to Background class. They didn't belong here

Revision 186 - (view) (annotate) - [select for diffs]
Modified Thu Jun 7 10:42:13 2007 UTC (17 years, 3 months ago) by duarte
File length: 3827 byte(s)
Diff to previous 182

FIXED BUG: The returned regex in motif2regex was wrong, needed a ".*" at the beginning

Revision 182 - (view) (annotate) - [select for diffs]
Modified Tue Jun 5 13:41:05 2007 UTC (17 years, 3 months ago) by duarte
File length: 3825 byte(s)
Diff to previous 181

FIXED BUG: the switch statement was missing the breaks
This was causing strange behaviour in counts NodeBackground getSize methods and also was making them being too slow

Revision 181 - (view) (annotate) - [select for diffs]
Modified Tue Jun 5 12:27:49 2007 UTC (17 years, 3 months ago) by duarte
File length: 3754 byte(s)
Diff to previous 179

New class NbhProbDistribution
In NodeNbh implemented a few static classes to convert between different motifs and to match motifs using differing criteria

Revision 179 - (view) (annotate) - [select for diffs]
Added Thu May 31 09:41:41 2007 UTC (17 years, 4 months ago) by duarte
File length: 1420 byte(s)

FIXED BUG: fixed restrictContactsToMax/MinRange. Couldn't delete contacts at the same time as looping in them
NEW CLASSES NodeNbh and EdgeNbh, now used in getNodeNbh and getEdgeNbh
New method getResidueType