General Help

• Click on a question mark icon will give additional information.
• Multiple items may be selected from the store by holding down the shift key when selecting. This allows easy viewing of multiple objects at once.

Frequently Asked Questions

• Why are the contents of the window is squashed together? The window needs to be enlarged. Next time that window appears it will assume the new size (it will not reset back to the squashed up size, unless the user makes it that size). After a number of attempts to get Java to automatically set the window to the correct size, I've given up for now (will be fixed once Java 2/Swing is facilitated).
• When do results in the Result Store get saved to disk? Whenever the store is changed, by adding or removing a object.
• What happens to the annotation of trees when I save them as a phylip/clustal file, or as a nexus file? It's lost.
• Is the sequence alignment code (Progressive Alignment) very powerful? No.
• What is the log actually for? The log window is a relic from earlier versions of Pebble. It may occasionly list debuging information, and unimportant information relating to the execution of a ceblet.
• What does "Force Garbage Collector" do? The "Garbage Collector" forces the freeing of unused memory by Pebble. It does not normally need to be used.
• Do I have to care what the "Startup Log" says? No.
• How do I change the background image? Look in the ApplicationTheme.properties file, find MainWindowTheme, and make an educated guess. Future versions of Pebble will make this easier.