fixed the while loop on the edge creation?
small code changes
fixed merge conflicts
cleaned main class, and few other code changes
added the correct name for cytoscape for the nodes
added cytoscape names for .ea and .sif files
Merge branch 'master' of https://github.com/merwanrambeau/pappl_bioinfo into merwanrambeau-master

Conflicts:
	src/MainTest.java
	src/Node.java
	src/SpecialNode.java
Tried to correct problems from merge. Not crashing but writing in files is not working.