Revision 372 - (view) (annotate) - [select for diffs]
Modified Wed Oct 31 10:20:22 2007 UTC (16 years, 11 months ago) by lpetzo
File length: 2978 byte(s)
Diff to previous 365

Revision 365 - (view) (annotate) - [select for diffs]
Modified Tue Oct 23 08:36:58 2007 UTC (16 years, 11 months ago) by duarte
File length: 2678 byte(s)
Diff to previous 352

New method getEdge in EdgeSet, necessary since we introduced weights in the Edge class. To retrieve them we first need to retrieve the actual Edge object

Revision 352 - (view) (annotate) - [select for diffs]
Modified Thu Oct 11 12:49:08 2007 UTC (16 years, 11 months ago) by stehr
File length: 2098 byte(s)
Diff to previous 336

Major redesign of NodeSet, now contains objects of new class Node. Nodes are essentially integer which can have additional properties. Added equals methods to NodeSet, EdgeSet, NodesAndEdges. Moved some methods from SimilarityGraph to NodesAndEdges.

Revision 336 - (view) (annotate) - [select for diffs]
Modified Tue Oct 2 16:14:20 2007 UTC (17 years ago) by stehr
File length: 1570 byte(s)
Diff to previous 234

extracted constant NULL_CHAIN_CODE from ...Pdb classes, added copy() methods to NodeSet and EdgeSet, added some functionality to NodesAndEdges, new class SimilarityGraph

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: 696 byte(s)
Copied from: trunk/proteinstructure/ContactList.java revision 231
Diff to previous 178

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

Revision 178 - (view) (annotate) - [select for diffs]
Modified Tue May 29 08:01:46 2007 UTC (17 years, 4 months ago) by duarte
Original Path: trunk/proteinstructure/ContactList.java
File length: 724 byte(s)
Diff to previous 175

Fixed bug in getMaxRange method, was not assigning to the max variable
Added toString method to Contact

Revision 175 - (view) (annotate) - [select for diffs]
Added Fri May 25 17:31:58 2007 UTC (17 years, 4 months ago) by duarte
Original Path: trunk/proteinstructure/ContactList.java
File length: 718 byte(s)

FIXED BUG in initialisation of fullLength when reading from file. In case of no sequence and nodes provided, was not getting correctly the maximum value for contacts. Now using the method getMaxContact from new class ContactList
NEW FUNCTIONALITY in Graph:
-New member variable modified
-New methods addEdge, delEdge, restrictContactsToMaxRange, restrictContactsToMinRange, getContacts, getNodes, copy
-Improved slightly the implementation of getEdgeNbh 
FIXED BUG in initialisation of fullLenght when reading from file. In case of no sequence and nodes provided, was not getting correctly the maximum value for contacts. Now using the method getMaxContact from ContactList
New class ContactList
NEW FUNCTIONALITY in Graph:
-New member variable modified
-New methods addEdge, delEdge, restrictContactsToMaxRange, restrictContactsToMinRange, getContacts, getNodes, copy
-Improved slightly the implementation of getEdgeNbh 
New method getRange in Contact