Monthly Archives: June 2009


Now we have the lab blog, everyone needs to post here all the time. We need to use it for sharing information with each other and our collaborators.

GenomeSearch Android App Update

The code is looking much better after Josh cleaned up it up and organized it. The current code is not displaying the genomes from the SEED and after testing it and trying to figure out exactly what the problem is, I’m finding that it has something to do with how we’re retrieving the text from the website and storing it. I was trying to find another way in reading in text from a website and then storing it because I’m not 100% sure on the method that’s being used right now so I need to talk to Josh to fully understand it. Other than that it seems the route we’re taking is working. I tested the setup of the code by using our test list and it performed perfectly.

Adding new content to the lab blog

When you add a new post to your lab blog, make sure to have the parameters set as follows:

Section: Lab blog

Category: Your name’s lab blog

Published: Yes

Show on Front Page: No

The rest of the configuration is up to you.

To make changes to a lab blog entry, click on the icon to the left of the entry title. (Make sure you are logged in order to see the icon).

Have fun adding content to the lab blog. 🙂

Restructured GenomeSearch Android app

Today (while I sat waiting to be called at jury duty for 7 hours…) I worked on restructuring the GenomeSearch program. It had become a bit of a cluttered mess since I originally made the class as a test class for putting pieces of tutorials together.

Now the program is laid out a lot more logically and in better OOP style. It took a fair bit of work, but I think that having a more sensible groundwork will keep our future work organized. I also worked a bit on getting the spinner to display the genomes from the seed, but this work is not complete just yet. I feel like what I’m uploading is pretty close to what Daniel and I need, however!

Using Subclipse

This guide is very useful for setting up Eclipse and Subversion to work together.

However, one issue that Daniel and I had today is that it is not immediately obvious how to check out a project if you aren’t the person who uploads it originally.

Clicking the Import option in the Eclipse package explorer results in a number of options being displaying. One of these should be SVN (if not it will be under ‘Other’). From this menu option, you can specify an svn directory online to check out a project from.

I’m still having some issues with getting Eclipse to be happy with things imported from our svn directory, however. I’ll try to remember to update this with the fixes when I find them!

Setting up Android development environment in Eclipse

This post will consist of mainly links to guides which I used in setting up my development environment to write Android apps.

Step 1. Install Eclipse as per usual (I always install the Classic package, but I’m not sure if that is the best way to go)

Step 2. Download the Android SDK (I don’t think it matters where you unzip it to, as long as you can find it later)

Step 3. Follow set up instructions

Step 4. Learn about how to create and run Android projects

A few gotchas:
Android has a built in JSON feature which is explained here:
Java does not ordinarily have JSON packages included (as far as I know), and if you include json_simple or similar packages, Eclipse will no longer recognize the Android JSON package.

This happened to me, and I had trouble figuring out how to tell Eclipse to ignore the package I no longer wanted. An easy work-around is to remake your project and copy/paste source files.

Add SVN project to Eclipse

So far Josh and I have discovered how to copy and save a project from the SVN repository into our own machine. We found two ways of doing so (I find the second method much faster):

1) Go to the Java Perspective and right-click in the Package Explorer. Click Import…, then in the Import screen click on the SVN folder and click on Checkout Projects from SVN. Click Next and then choose the correct repository location. Click Next and choose the folder containing the project and click Next (if you wish to change the project name, workspace, or other revisions) or you can click Finish. This will import the project and its contents into your machine.

2) Go to the SVN Repositories Perspective and right-click on the folder containing the project and choose Checkout…. This will bring you to the screen where you can edit the Project Name and workspace location. Afterwards, click Finish and your project will be imported into your machine.


The other problem I was having was after I would import the project into Eclipse is that I would get these errors showing on my Console tab. The error would say something about “Classfiles missing” and under my Problems tab an error saying “Path files not found” would also show. I resolved the issue by simply clicking on Project at the top of the screen and then choose Clean… So far it has been successful but I am looking for any other consequences this may have caused.

So far with Genome Search…

So I’m going to go ahead and write what I’ve been working on today so far. Not sure if this is exactly what the lab-blog is for but here it goes:

Finally it seems as though the SVN problem has been fixed. The previous problem was that I did not know how to import the project into eclipse but I figured out two ways to do so. Also, I was receiving a sort of “classfile missing” and “path files were not found” type of error but I just did a few simple actions which fixed it. I will post a separate blog describing these.

Other than that, I have been researching different methods to add the list of names to the spinner-drop-down-menu. One method that I’m set on that might work is using the ArrayAdapter constructor instead of the createFromResource method to fill in the spinner. I successfully displayed arbitrary Strings to display on it using the constructor and now I’m attempting to parse the String from the genomes website into an array and then putting only the names into a String array. That is where I am stuck. It seems as though the myString variable that’s supposed to be holding the content from the genomes website is either not parsing correctly or the content isn’t being stored in myString variable correctly. I’m planning on continuing this tomorrow so Josh and I could figure this out.

SEED annotators call

The time of the weekly SEED annotators conference call/WebEx.

I’m trying to see if I can take notes here.

* Among the issues being discussed is:

– problems with annotating ABC transporters

– problems with multifunctional proteins

– problems with frameshifts and short ORFs