More updates. working on comparisons
topological overlap updates
Merge remote-tracking branch 'origin/fixedTOM'

Conflicts:
	NetworkCalculator/src/networkCalcPackage/NetworkCalculator.java
	NetworkCalculator/src/networkCalcPackage/Operations.java
This is a test commit from Netbeans
Testing the removal of the change made earlier
Major updates. added Clustering class based on hierarchical-clustering-java git
More major updates. first with netbeans (stupid eclipse)

Fixed name problems.
Minor fixes
Beginning of linear matrix representation - needs more development
Fixed threading. TOM problems remain.