Hi lauren.

I just put a demonstration up on my blog.

Ok. I''ve added an automatically updated build of your project to our system, an posted links to the webstart and InstallAnywhere outputs. This is updated directly from the googlecode repository, so if you commit any changes, the version will be updated automatically.
I can't make the server that does the builds accessible to you, but you can at least view the logs for each build in the logs directory:

You mentioned something
about this in a previous email, but I couldn't figure out how to
remove the bug for the annotation display of helices for the backward
arrows. I can't get the arrows to show up in a consistent place
either. I'm a bit mystified about how the variable "lastSSX" is
computed at this step, because I keep getting that it equals 0 when it
goes through this part of the switch statement. Perhaps we can talk
about this after I've finished the description for the newsletter.

yes. though here's some pointers about the rendering logic in the second switch statement that might help you out:

  * the lastSS variable gets set to the last secondary structure symbol rendered (i.e. the one to the left of the final position being rendered in the second switch statement).
  * The logic for the beta strand rendering code, you should see that it is only deciding whether to put an right-arrow head should be rendered or not.
  * For rna secondary structure arrows the logic is more complex: you need to use lastSS to decide if you are at the end of a left-arrow (in which case, you draw the body of the arrow only), in the middle of an arrow (ie both the previos and the next annotation element exists and is part of the same stem), or at the end of a right-arrow (which is the same logic as the beta sheet symbol).

I suggest you take a careful look at the rendering code again, and see if you can spot what you need to do in order to get the arrows rendering properly when the horizontal scroll bar is moved. If you really can't work it out, then we could talk about it next week,

Should I just say that these features will be included in the next
release of Jalview or should I make a JAR file available? I tried to
export my eclipse project as a jar, but there were some compile
errors, so I need some guidance on how to do this correctly.

The ant build script includes all the mechanisms you need to build a webstart version of jalview. You'll need to set up a new build task that executes the 'makefulldist' ant target, and you'll also need to make a key to sign the jars using the java key tool. See the page in doc/building.html for the instructions on how to do this. However, if you're happy with the automated build URL that I've set up, then you probably don't need to do this - except for local/in lab testing!



On 19/08/2010 07:22, Lauren Lui wrote:

J. B. Procter (JALVIEW/ENFIN) Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764
The University of Dundee is a Scottish Registered Charity, No. SC015096.

Clearly my grammar is broken when I write about program logic..:


On 20/08/2010 10:30, Jim Procter wrote:

* The logic for the beta strand rendering code, you should see that it
is only deciding whether to put an right-arrow head should be rendered
or not.

That point should be:
"The beta strand rendering logic is only deciding whether to put a right-arrow head at the last rendering position or not."

but I suspect you worked that out anyway :slight_smile: