Implemented Empty Vertices + Mutation Indication and Graph display in GUI

[joswinter]

Mutation indication is working, implemented the graph display into the GUI with some mock data. Alignment is still skewed because of the sorting of the edges on destination start position.
#13: Insert empty nodes (insertion / deletion) in DNA sequence graph
#15 Indicate mutation types based on empty tiles and relative

coordinates (insertion, deletion and SNP)

[jorenham]

You should mark the obsolete methods/classes with @Deprecated

DefaultGraphParser.java:125
You create a new SegmentString, this clashes with dependency injection; you should pass a SegmentString factory to the method

TileView.sequenceColor
The color code constants should be (static) final fields. Better yet, use css for this by setting the styleclass and putting the color for the styleclasses in the css file.

Vertex.java
This class is a view, so it should be named that way.

[alangerak]

TileView.sequenceColor
It is better practice to use either overloading methods or make a method in the interface of mutation and implement those in the relevant mutation classes.

[joswinter]

We should wait with implementing the style into a stylesheet. It would be best to do this in a whole in a later pull request. I will create an issue for that.

Fixed most of the remarks for the pull request, so can be merged.