Presets allow you to store commonly used settings for url links, colors, and other settings. This allows you to quickly apply commonly used settings to different documents. Moreover, the default preset is the setting which a new file gets. Presets are not specific to any document, which means they can be edited when no files are loaded.

Url Presets

Figure 2.1. Url Presets Dialog

Url Presets Dialog

Url Presets are the only presets which apply to many views, since url linking is a view-independant process. Java TreeView stores the url presets for arrays and genes separately, thus there are two sets of url presets, gene url presets and array url presets, which are treated essentially the same.

Java TreeView supports linking to external databases. In a Dendrogram or Karyoscope, clicking on a gene will cause a corresponding database page to be loaded in an external browser. Dendrogram also supports linking by array. Exactly what database page gets loaded depends on the Url Settings. The exact mechanism for load depends on the operating system, and can be a source of url bugs (see Chapter 3).

URL Presets allow you to store presets for databases you may wish genes and arrays to link to. There are several default presets which come with Java TreeView. You can delete or modify all of them, as well as add additional presets.

There is a special preset which disables linking. You can set this as the default url preset to avoid spurious linking.

Dendrogram Color Presets

Figure 2.2. Dendrogram Color Presets Dialog

Dendrogram Color Presets Dialog

This set of presets allow you to configure preset color schemes for the dendrogram component. It is also referred to as just color presets in TreeView, since there's no other views which could have color settings.

Karyoscope Coordinates Presets

Figure 2.3. Karyoscope Coordinates Presets Dialog

Karyoscope Coordinates Presets Dialog

Stores a list of frequently used coordinates files. In addition to using a particular preset,it is also possible to parse the pcl or cdt file itself for the coordinates. Selecting "None" makes this the default behavior.