Adding Directionality

[ntalluri]

Closes #107

[ntalluri]

Update Summary.py For Mixed Graphs #128

[agitter]

Now that we can support mixed graphs, I can update the EGFR example network to the original version that included directed and undirected edges. I'll need to adjust the edge weight that was greater than 1 again. The file came from https://raw.githubusercontent.com/koksal/tps/master/data/networks/phosphosite-irefindex13.0-uniprot.txt

[agitter]

I merged the Cytoscape changes and resolved merge conflicts in 39b4748. We can extend Cytoscape to support the U and D edge types in the pull request and then update the image to v2.

[agitter]

I continued reviewing and made it through all of the source files under the spras directory.

[agitter]

I finished reviewing the rest of the files in the pull request.

[agitter]

I ran the algorithms with the EGFR test data as a final test, which nicely illustrates outputs on a mixed graph. That revealed some problems with self-edges in the dataset that MEO couldn't handle, so I removed them. I also noticed the edge direction support in Cytoscape wasn't working yet, so I rebuilt and pushed the updated Docker image. That didn't fix the problem:

I believe it is because there isn't a header row. We will add support for that later (#4 (comment)) and then can retest this.

b4d6e1c contains changes from my final proofreading and formatting. If the tests pass, I'll merge.