Re: [Jtreeview-devel] What is the best way to add more functions/panels?

[Alok S. <al...@ca...>]

Hi Xiaoqing,

First, let me say that I don't really understand what you want to do-=20
it is hard to get a sense for it over email. In general, I recommend=20
that you write a new "View". There are already several views, such as=20
dendroview, karyoview, scatterview, and treeanno. Each view is defined=20=

in it's own package. The main class for each view implements MainPanel,=20=

i.e.

Dendroview: edu.stanford.genetics.treeview.dendroview.Dendroview.java
Karyoview: edu.stanford.genetics.treeview.karyoview.KaryoPanel.java
Scatterview:=20
edu.stanford.genetics.treeview.scatterview.ScatterPanel.java
Tree Annotation:=20
edu.stanford.genetics.treeview.treeanno.TreeAnnoPanel.java


I recommend that you define a new view in a new package. The package=20
need not begin with edu.stanford.genetics.treeview, but the main class=20=

of your view must implement MainPanel. Since your view is likely very=20
similar to the dendroview, you can either copy over the classes into=20
your package, or just reference the relevant parts. If you find that=20
you must modify something, just copy the code over.
I recommend that you add new annotation columns or rows in the CDT file=20=

with special column/row names that only your View uses, and that you=20
put all specific data for your view in those columns or rows. This will=20=

ensure that the standard DataModel can load your data and make it=20
available to your View.

Once you have defined your main class, you just need to add an option=20
for it to edu.stanford.genetics.treeview.LinkedPanel. It should be=20
straightforward, as there are only a few parts of LinkedPanel that=20
depend upon knowing what views exist. After you have done this, you can=20=

open up your custom view using "Analysis->Your view". Alternatively,=20
you can make your view the one that is loaded by default by=20
LinkedPanel, by editing the setupRunning method or one of the functions=20=

it calls.

I am sorry that this is so complicated. By the end of the year, I hope=20=

to transition to a plugin-style architecture. In the new architecture,=20=

Java Treeview will be split into a small kernel and a variety of=20
plugins, one plugin for each View. Each plugin will be distributed as a=20=

separate jar file, and Java Treeview will load all the plugins at=20
startup. The user will be able to change the plugin that is used by=20
default, so they won't have to continually select "Analysis->Your=20
View".  Once that transition is complete, you will be able to make your=20=

View available as a jar file plugin that people can download and use=20
with the standard Treeview distribution simply by copying it to the=20
"plugins" folder. The user will also be able to delete the jar files=20
for plugins that they seldom use. Until then, I recommend that you=20
maintain a separate source tree for your organization, and distribute=20
your modified version to whoever needs it.

I am willing to consider adding your functionality to the main=20
Dendroview component. However, I would prefer that you implement it=20
first, with maximum freedom to add the features you want, and then=20
later on we can consider whether to add it to Dendroview or keep it as=20=

a separate plugin.

I hope that this is enough to get you started.

	-Alok

On Mar 15, 2005, at 2:30 PM, Xiaoqing Zhang wrote:

> Hi Alok,
>
> =A0
>
> This is Xiaoqing Zhang from Columbia University. I am a Java=20
> programmer and work for Dr. Christina Leslie. We want to add some=20
> functions in the JTV. The idea is after it opens a .cpt file, we hope=20=

> JVT can load some additional files which contain upstream regulatory=20=

> motif of each probe or such information can be included in the .cpt=20
> file too. An additional Gene Panel will be created. =A0Then when the=20=

> mouse moves over some probes, in the gene panel, it will display a=20
> line with colored motif in it for each selected gene. =A0I did not see=20=

> any similar thing in the current JTV. I just wonder whether you can=20
> give me some suggestions about how to do it. I know I may change the=20=

> GUI of your JTV and I do not want to disrupt more things than=20
> absolutely necessary.
>
> =A0
>
> =A0
>
> Thanks a lot for your attention.
>
> =A0
>
> =A0
>
> =A0
>
> =A0
>
> Xiaoqing