Re: [Jtreeview-users] Highlighting specific edges in JTV

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

Hi Itamar,

First of all, you should look at this example:

http://jtreeview.sourceforge.net/examples/index.html#ex5

You can probably achieve the display that you want by actually hard- 
coding the colors in the GTR (gene tree) file. For example,

> NODEID	LEFT	RIGHT	CORRELATION	NODECOLOR
> NODE1X	GENE2268X	GENE2269X	0.989404	#9900FF

This indicates that the node named "NODE1X" which is formed by  
joining "GENE2268X" and "GENE2269X" should be colored "#9900FF" or  
bright purple.

However, rather than preprocessing the GTR files and adding a column,  
you may want to add functionality to do this on the fly. The best way  
to do this is to write a plugin. I have written an example plugin  
that you should be able to read through as it is under 200 lines of  
code:

https://sourceforge.net/docman/display_doc.php? 
docid=35149&group_id=84593

Your plugin shouldn't be too hard, depending on how exactly the  
coloring works. Here's one scheme that could work:

1) Write a class that extends PluginFactory. Look at the code for  
DataTableFactory from the example plugin to see how easy it can be.  
There are two ways you could make it work:
1a) The selection of the file and coloring of the tree can happen  
within dialogs triggered by restorePlugin, which would then return  
null, or
1b) restorePlugin returns a MainPanel that has a button that opens a  
file search dialog to locate the file with the color info, and a  
second button that loads it.
The advantage of 1b is that you can then have a list of common  
presets, if there are particular sorts of colorings you use often

2) Your write a method either in the PluginFactory or MainPanel that  
gets called with two parameters, 1) the name of the file with the  
coloring info, and 2) The viewFrame reference that was passed in to  
restorePlugin. It loads up the coloring info, and then calls  
viewFrame.getDataModel().getGtrHeaderInfo() to get the HeaderInfo  
representing the headers for the gene tree.

3) Call HeaderInfo.getHeaderIndex("NODECOLOR") to see if column  
exists, if not call HeaderInfo.addName("NODECOLOR", getNumHeaders()),  
and check to make sure it returns true.

4) Traverse the gene tree headers to figure out which nodes to color  
what, and then call HeaderInfo.setHeader(nodeNumber, "NODECOLOR",  
"#9900FF"), with the appropriate node number and color of course.

This may or may not work as planned... in particular, the updates  
from calling setHeader may not propagate all the way, as I don't have  
a plugin that works in quite this way yet. If you think it would be  
helpful, I could write up a quick test plugin that implements the  
above four steps and colors the nodes using a user-specified  
correlation threshold on the fly- i have been meaning to do this at  
some point anyways.

I should also mention that you can get access to the state and data  
structures of the dendrogram (and in particular its in-memory tree of  
TreeDrawerNodes) by calling viewFrame.getMainPanelsByName 
("Dendrogram"). it's straightforward, but a little more coding  
(although less coding than building your own tree of TreeDrawerNodes).

All of the above only applies to the version of the code checked into  
CVS, there are a number of fixes made since the last release... in  
fact, I was planning to do a new release soon, since there are a few  
big problems in the last release. If there are any issues that need  
to be addressed for your plugin, it would be nice to do it before then.

	-Alok


On Feb 13, 2007, at 12:53 PM, Itamar Cohen wrote:

> Hi Alok,
>
> First of all, thanks for your response about height of subtrees, it  
> was very helpful.  We have a project now in which we are trying to  
> highlight specific edges in a tree.  I'm trying to alter the JTV  
> code so it would read a list of node pairs and would show these  
> edges in a different color.  Could you suggest a simple way to  
> enable this?
>
> Thanks,
> Itamar
>
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