Revision 238 - (view) (annotate) - [select for diffs]
Modified Fri Jul 20 10:02:03 2007 UTC (17 years, 2 months ago) by duarte
File length: 1032 byte(s)
Diff to previous 234

Optimised slightly the compareTo method in Edge

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: 964 byte(s)
Copied from: trunk/proteinstructure/Contact.java revision 231
Diff to previous 224

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

Revision 224 - (view) (annotate) - [select for diffs]
Modified Thu Jul 5 13:42:37 2007 UTC (17 years, 2 months ago) by duarte
Original Path: trunk/proteinstructure/Contact.java
File length: 982 byte(s)
Diff to previous 185

Now calculate distance matrix uses HashMap instead of TreeMap
Needed to change the hashCode function in Contact to make it faster

Revision 185 - (view) (annotate) - [select for diffs]
Modified Thu Jun 7 09:14:46 2007 UTC (17 years, 3 months ago) by duarte
Original Path: trunk/proteinstructure/Contact.java
File length: 930 byte(s)
Diff to previous 178

Implemented hashCode method in Contact and GenericContact. Was necessary to use these classes as keys in Maps
Fixed bug in equals method in GenericContact
Changed middle character from "\t" to " " in toString

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/Contact.java
File length: 789 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]
Modified Fri May 25 17:31:58 2007 UTC (17 years, 4 months ago) by duarte
Original Path: trunk/proteinstructure/Contact.java
File length: 727 byte(s)
Diff to previous 123

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

Revision 123 - (view) (annotate) - [select for diffs]
Added Wed May 9 10:45:53 2007 UTC (17 years, 4 months ago) by duarte
Original Path: trunk/proteinstructure/Contact.java
File length: 664 byte(s)

Initial commit of the proteinstructure package. Contains classes to use pdb protein structures