Up and Running!

28 05 2008

After a few days of discussion on the cytoscape-discuss google group, I’ve finally managed to run a simple plugin in Eclipse (from a separate project) that will work with the other Cytoscape source code (Special Thanks to Piet Molenaar for the patience and assistance!). Now I can also debug plugins in Eclipse!

Now that I’ve got my programming environment correctly set up (hopefully), the next step will be to start on Subproject 1. For details on this subproject, please visit the About page.


Setting Up Eclipse

27 05 2008

In the last post, I mentioned that I was having trouble getting the Cytoscape source code to run in Eclipse because I was missing libraries. It turns out that the cytoscape.bookmarks library files are generated at runtime (this I learned from the cytoscape-discuss board). However, I was still unable to run the Cytoscape program on Eclipse. As a solution, I installed the Subclipse plugin for Eclipse which allows for subverision from within Eclipse. I created a Java Project from Subclipse, and installed Jakarta Ant (which is necessary to build Cytoscape, as mentioned in the README file that can be found in the repository), and I managed to get the source code up and running! :)

By the end of last week and Monday of this week, I started focusing on learning more about Ant. I’ve been reading:

Java Development with Ant – By Erik Hatcher and Steve Loughran

Ant – The Definitive Guide – By Steve Holzner

It turns out that Ant isn’t that hard to pick up if you know XML and Java (and Make for C and C++ projects).

Today, and for the next few days, I have and will continue to try to debug a simple plugin in Eclipse. I’ve followed the “Setting Up Eclipse For Plugin Development” tutorial, but I still have a few issues that I will have to work out before I can say I can entirely debug plugins in Eclipse.

By the way, I’ve added a “Progress” page to this blog to make tracking the progress of this project easier.

Getting Started

16 05 2008

This week is my first week working on this Cytoscape project. I’ve spent the majority of my week familiarizing myself with the Cytoscape program, and reading their Contents page to acquire a better understanding on the graph layout algorithms that it uses.

By the end of this week, I’ve started reading the source code of classes that are relevant to the plugin that I plan to program this summer. At the same time, I have attempted to try to run the source code on Eclipse. However, I have 100 errors (and yes, exactly 100) complaining about the missing cytoscape.bookmarks library. I am going to continue reading/asking on the cytoscape-discuss group, and hope to find a solution to this problem as soon as possible.

About the Project

16 05 2008

IDEA 21: Automatic (Smart) Node and Edge Label Layout

Cytoscape is currently capable of reorganizing (selected) nodes and edges of a graph into different forms using various layout algorithms. These layout algorithms are currently only capable of organizing the graph so that there is an adequate amount of room between the nodes. However, these algorithms have not taken the labels that the user may wish to assign to certain nodes and edges into consideration, which has greatly decreased the clarity and legibility of more complex graphs, and graphs where larger labels are required.

Hence, my job this summer is to integrate an algorithm with Cytoscape’s existing layout algorithms that will allow labels to be added to the graph while maintaining the graph’s general legibility.