Removed specific regex for uniprot ids in order to apply teh code to EntrezGene ids.
EntrezGene can now be seen on the graph
rna molecule type is handled
Changed the .gitignore file to ignore the Eclipse .metadata file.
Adapted the EntrezGeneID (or GeneID) in the AffymetrixRegexReaderFile.
New changes to consider EntrezGene.
Removed class diagram.
Tests for .jar version of the plugin
Implemented the IlluminaRegexReader class (was mainly just a copy of AffymetrixRegexReader before)
Implemented the view and the controller of Illumina
Still some issues :
- null pointer exceptions
- when the step 2 is used with an Illumina file, no node is suppressed.
Fixed the illumina process.
Changing on Illumina file reading.
Tryed to fix the step 3 bug for the .jar. It is still not working.
Changed the Illumina view.
Merge branch 'ThomasBrunelBranch'

Conflicts:
	ProjetCytoscape/src/main/java/de/bioquant/cytoscape/pidfileconverter/FileReader/AffymetrixRegexReader.java
	ProjetCytoscape/src/main/java/de/bioquant/cytoscape/pidfileconverter/FileReader/IlluminaRegexReader.java
	ProjetCytoscape/src/main/java/de/bioquant/cytoscape/pidfileconverter/FileReader/MoleculeHandler.java