Introduction
This is a short description of the program SoupViewer.
SoupViewer was developed to give a more comfortable way of analyzing the big trees which come from RNAsoup.
Installation
Just download (new version, advanced text search, 8.5.) the file SoupViewer-0.7.5.2.jar.
You will additonaly need some kind of java on you computer.
Start the programm
You can start the jar-file through "java -jar SoupViewer-0.7.5.2.jar"
There are two parameters for the SoupViewer
- -t a tree-file in xml-format (necessary)
- -i a directory with additional alignment pictures (as .gif or .jpg)
For example:
java -jar SoupViewer-0.7.5.2.jar -t pathToTree/myTree -i pathToAligs/aligs/
Important: If you get an OutOfMemoryError you need to assign more Memory to Java. You can do this with
java -Xmx -jar SoupViewer-0.7.5.2.jar -t pathToTree/myTree -i pathToAligs/aligs/
Usage
Zoom
On the left side of the frame you see a ZoomBox(1). Here you can choose a zoom factor after pressing the "update"-Button the Tree will be repaint. Increasing the zoom level extends the distance between the nodes so its more easy to look at a special part of the tree.
NodeButton
In the tree there is a Button for every node(2). If you push this button this will open a new Frame with some information about this node.
If you move the mouse over one of the pictures it becomes larger, if you click on the picture it will stay large till the next click on it.
ColorBars
On the right side you see some coloured bars(3). There are three colorbars each of them can be adjusted with a different k-value through the Combobox(4) at the bottom.
In a colorbar you see all groups for the given k-value in the tree through the three different colors. For every group there are two additional pictures which you can open per click on it.
If there are less than 200 pictures for a colorbar there are two miniatures of the pictures beside the bar. Otherwise there are just some buttons like the NodeButtons.
Find leaf
You can search for leaves throug the shortcut "CTR+F" or "Edit->Find Leaf" in the title menu. Every leaf which contains the give string will be highlighted.
Contact
If you have any kind of problems or suggestions how to improve the SoupViewer feel free to send a mail to jane@bioinf.uni-leipzig.de