recording hierarchical tree

[yy]

To draw the corresponding hierarchical tree (dendrogram), the program should record the hierarchical information to the file. I think this feature is not so important for the C++ version that deals with larger networks.

[bagrow]

I added some very basic dendrogram recording to the develop branch (commit 0c41c2b....).

This may be sufficient to get a dendrogram, but it will take a lot of work to go from the new output to a plotted dendrogram, so I do not yet consider this closed!

[yy]

To record dendrogram, we may need to use alternative way to assign community id. How about making a class Dendrogram to keep the linkage and export with a couple of different formats? There are several formats for dendrogram:

• matlab linkage file
  • http://www.mathworks.com/help/toolbox/stats/linkage.html
• gtr, atr file (mainly used for microarray visualization)
  • http://bonsai.hgc.jp/~mdehoon/software/cluster/manual/Hierarchical.html
  • http://jtreeview.sourceforge.net/docs/JTVUserManual/ch02s11.html
  • http://jtreeview.sourceforge.net/examples/#ex1