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

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

Ah, it seems I misunderstood your question. Currently, there is no =20
way to represent relationships between pairs of nodes in java =20
treeview. I can think of two ways to do it:

1) The hard way to do it that would be in keeping with the java =20
treeview design would be to introduce some interface like HeaderInfo =20
that would capture the pairwise relationships on the nodes, add a =20
method to DataModel that makes it possible to retrieve the data =20
structure, and then modify the TreeDrawer to make use of it. You =20
would also have to introduce a new file format to keep track of =20
pairwise node relationships.

2) A much easier solution would be to add "LEFTCOLOR" and =20
"RIGHTCOLOR" columns to the GTR/ATR files, and then hack TreeColorer =20
and TreeDrawer to make use of those columns when "NODECOLOR" is not =20
present. You would also need to add two fields to TreeDrawerNode to =20
hold the left and right colors. If all three colors are present, you =20
could color the base of the node with NODECOLOR and the two branches =20
with the left and right.

I would recommend #2, unless you plan on doing a lot with pairwise =20
node relationships, in which case #1 may pay off eventually. Let me =20
know if you plan to implement one of these, or something rather =20
different. #2 has the advantage that it could be implemented entirely =20=

as a standalone plugin- just copy over the plugin/dendrogram source =20
tree and subclass TreeDrawerNode in the plugin, and use it when you =20
build the tree in TreeDrawer.setData(). If/when I adsorb it back into =20=

the main source tree, I should be able to just overwrite the base =20
class with your TreeDrawerNode, and update the relevant classes in =20
plugin/dendrogram. Changing colors on the fly would work as described =20=

in my previous email.

	-Alok

On Feb 20, 2007, at 7:20 AM, Itamar Cohen wrote:

> Hi Alok,
> First of all, thanks for the quick response.  As I understood from =20
> your response the only way to change colors is by changing the =20
> color of both edges coming out of the node (changing the color of =20
> A  B  C will change both the edges AB and AC).  Is there a way to =20
> only change the color of one of them?
>
> Thanks,
> Itamar Cohen
>
> CC: jtr...@li...
> From: al...@ca...
> Subject: Re: Highlighting specific edges in JTV
> Date: Tue, 13 Feb 2007 15:21:28 -0800
> To: co...@ho...
>
> 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-=20=

> 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 =20
> joining "GENE2268X" and "GENE2269X" should be colored "#9900FF" or =20
> bright purple.
>
> However, rather than preprocessing the GTR files and adding a =20
> column, you may want to add functionality to do this on the fly. =20
> The best way to do this is to write a plugin. I have written an =20
> example plugin that you should be able to read through as it is =20
> under 200 lines of code:
>
> https://sourceforge.net/docman/display_doc.php?=20
> docid=3D35149&group_id=3D84593
>
> Your plugin shouldn't be too hard, depending on how exactly the =20
> coloring works. Here's one scheme that could work:
>
> 1) Write a class that extends PluginFactory. Look at the code for =20
> DataTableFactory from the example plugin to see how easy it can be. =20=

> There are two ways you could make it work:
> 1a) The selection of the file and coloring of the tree can happen =20
> within dialogs triggered by restorePlugin, which would then return =20
> null, or
> 1b) restorePlugin returns a MainPanel that has a button that opens =20
> a file search dialog to locate the file with the color info, and a =20
> second button that loads it.
> The advantage of 1b is that you can then have a list of common =20
> presets, if there are particular sorts of colorings you use often
>
> 2) Your write a method either in the PluginFactory or MainPanel =20
> that gets called with two parameters, 1) the name of the file with =20
> the coloring info, and 2) The viewFrame reference that was passed =20
> in to restorePlugin. It loads up the coloring info, and then calls =20
> viewFrame.getDataModel().getGtrHeaderInfo() to get the HeaderInfo =20
> representing the headers for the gene tree.
>
> 3) Call HeaderInfo.getHeaderIndex("NODECOLOR") to see if column =20
> exists, if not call HeaderInfo.addName("NODECOLOR", getNumHeaders=20
> ()), and check to make sure it returns true.
>
> 4) Traverse the gene tree headers to figure out which nodes to =20
> color what, and then call HeaderInfo.setHeader(nodeNumber, =20
> "NODECOLOR", "#9900FF"), with the appropriate node number and color =20=

> of course.
>
> This may or may not work as planned... in particular, the updates =20
> from calling setHeader may not propagate all the way, as I don't =20
> have a plugin that works in quite this way yet. If you think it =20
> would be helpful, I could write up a quick test plugin that =20
> implements the above four steps and colors the nodes using a user-=20
> specified correlation threshold on the fly- i have been meaning to =20
> do this at some point anyways.
>
> I should also mention that you can get access to the state and data =20=

> structures of the dendrogram (and in particular its in-memory tree =20
> of TreeDrawerNodes) by calling viewFrame.getMainPanelsByName=20
> ("Dendrogram"). it's straightforward, but a little more coding =20
> (although less coding than building your own tree of TreeDrawerNodes).
>
> All of the above only applies to the version of the code checked =20
> into CVS, there are a number of fixes made since the last =20
> release... in fact, I was planning to do a new release soon, since =20
> there are a few big problems in the last release. If there are any =20
> issues that need to be addressed for your plugin, it would be nice =20
> 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 =20=

> was very helpful.  We have a project now in which we are trying to =20
> highlight specific edges in a tree.  I'm trying to alter the JTV =20
> code so it would read a list of node pairs and would show these =20
> edges in a different color.  Could you suggest a simple way to =20
> enable this?
>
> Thanks,
> Itamar
>
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