Once you have downloaded and unpacked the distribution, you should be confronted with a set of files similar to those listed in Figure 1.1, “Contents of Java TreeView Distribution Archive”. Before reading further, you should run the TreeView.jar program to make sure your installation works. At this point, you might want to view a sample cdt or pcl file to get the hang of how it works. You can grab one from the examples section of the website or skip ahead to the file formats section (Chapter 2, Feature Reference, the section called “File Formats”) if you aren't sure whether your file is properly formatted.

Java TreeView offers many views of the data which are linked together.

In all these views there are visual cues to show which genes are selected. Any operation which selects genes in one view, either due to genome ordering, hierarchical clustering, or per-gene statistics, selects the genes in all views. This is because the application only maintains one list of selected genes. This list of selected genes can also be used to create exported images and data files such as gene lists and sub-pcl files using the Export features, documented in chapter 2.